gebhart/patrepeval huggingface dataset:
Towards Green Ammonia Synthesis through Plasma‐Driven Nitrogen Oxidation and Catalytic Reduction (2020)

Abstract Ammonia is an industrial large‐volume chemical, with its main application in fertilizer production. It also attracts increasing attention as a green‐energy vector. Over the past century, ammonia production has been dominated by the Haber–Bosch process, in which a mixture of nitrogen and hydrogen gas is converted to ammonia at high temperatures and pressures. Haber–Bosch processes with natural gas as the source of hydrogen are responsible for a significant share of the global CO 2 emissions. Processes involving plasma are currently being investigated as an alternative for decentralized ammonia production powered by renewable energy sources. In this work, we present the PNOCRA process (plasma nitrogen oxidation and catalytic reduction to ammonia), combining plasma‐assisted nitrogen oxidation and lean NO x trap technology, adopted from diesel‐engine exhaust gas aftertreatment technology. PNOCRA achieves an energy requirement of 4.6 MJ mol −1 NH 3 , which is more than four times less than the state‐of‐the‐art plasma‐enabled ammonia synthesis from N 2 and H 2 with reasonable yield (&gt;1 %).
Kinetic Analysis of tRNA-Directed Transcription Antitermination of the Bacillus subtilis glyQS Gene In Vitro (2004)

Binding of uncharged tRNA to the nascent transcript promotes readthrough of a leader region transcription termination signal in genes regulated by the T box transcription antitermination mechanism. Each gene in the T box family responds independently to its cognate tRNA, with specificity determined by base pairing of the tRNA to the leader at the anticodon and acceptor ends of the tRNA. tRNA binding stabilizes an antiterminator element in the transcript that sequesters sequences that participate in formation of the terminator helix. tRNA(Gly)-dependent antitermination of the Bacillus subtilis glyQS leader was previously demonstrated in a purified in vitro assay system. This assay system was used to investigate the kinetics of transcription through the glyQS leader and the effect of tRNA and transcription elongation factors NusA and NusG on transcriptional pausing and antitermination. Several pause sites, including a major site in the loop of stem III of the leader, were identified, and the effect of modulation of pausing on antitermination efficiency was analyzed. We found that addition of tRNA(Gly) can promote antitermination as long as the tRNA is added before the majority of the transcription complexes reach the termination site, and variations in pausing affect the requirements for timing of tRNA addition.
Eradication of chemotherapy‐resistant CD44+ human ovarian cancer stem cells in mice by intraperitoneal administration of clostridium perfringens enterotoxin (2011)

CPE may represent an unconventional, potentially highly effective strategy to eradicate chemotherapy-resistant cancer stem cells.
Iterative Design and Evaluation of a Tangible Robot-Assisted Handwriting Activity for Special Education (2020)

In this article we investigate the role of interactive haptic-enabled tangible robots in supporting the learning of cursive letter writing for children with attention and visuomotor coordination issues. We focus on the two principal aspects of handwriting that are linked to these issues: Visual perception and visuomotor coordination. These aspects, respectively, enhance two features of letter representation in the learner's mind in particular, namely the shape (<i>grapheme</i>) and the dynamics (<i>ductus</i>) of the letter, which constitute the central learning goals in our activity. Building upon an initial design tested with 17 healthy children in a preliminary school, we iteratively ported the activity to an occupational therapy context in 2 different therapy centers, in the context of 3 different summer school camps involving a total of 12 children having writing difficulties. The various iterations allowed us to uncover insights about the design of robot-enhanced writing activities for special education, specifically highlighting the importance of ease of modification of the duration of an activity as well as of adaptable frequency, content, flow and game-play and of providing a range of evaluation test alternatives. Results show that the use of robot-assisted handwriting activities could have a positive impact on the learning of the representation of letters in the context of occupational therapy (<i>V</i> = 1, 449, <i>p</i> < 0.001, <i>r</i> = 0.42). Results also highlight how the design changes made across the iterations affected the outcomes of the handwriting sessions, such as the evaluation of the performances, monitoring of the performances, and the connectedness of the handwriting.
ACE inhibitors in acute and chronic ischaemia: current status and future promise. (1989)

1. Myocyte loss, reactive hypertrophy, dynamic ischaemia with 'stunning', and ventricular wall remodelling are all involved in the initiation and progression of myocardial failure which is ischaemic in origin. 2. The effects of ACE inhibitors to reduce preload and afterload has potentially salutary effects in these settings. Moreover, sulphyl containing ACE inhibitors may have further actions in reducing free radicals and their damage in the acute phases of these events. 3. These promising initial studies warrant further exploration.
Allosteric role of a structural NADP + molecule in glucose-6-phosphate dehydrogenase activity (2022)

Human glucose-6-phosphate dehydrogenase (G6PD) is the main cellular source of NADPH, and thus plays a key role in maintaining reduced glutathione to protect cells from oxidative stress disorders such as hemolytic anemia. G6PD is a multimeric enzyme that uses the cofactors β-D-glucose 6-phosphate (G6P) and "catalytic" NADP<sup>+</sup> (NADP<sup>+</sup>c), as well as a "structural" NADP<sup>+</sup> (NADP<sup>+</sup>s) located ∼25 Å from the active site, to generate NADPH. While X-ray crystallographic and biochemical studies have revealed a role for NADP<sup>+</sup>s in maintaining the catalytic activity by stabilizing the multimeric G6PD conformation, other potential roles for NADP<sup>+</sup>s have not been evaluated. Here, we determined the high resolution cryo-electron microscopy structures of human wild-type G6PD in the absence of bound ligands and a catalytic G6PD-D200N mutant bound to NADP<sup>+</sup>c and NADP<sup>+</sup>s in the absence or presence of G6P. A comparison of these structures, together with previously reported structures, reveals that the unliganded human G6PD forms a mixture of dimers and tetramers with similar overall folds, and binding of NADP<sup>+</sup>s induces a structural ordering of a C-terminal extension region and allosterically regulates G6P binding and catalysis. These studies have implications for understanding G6PD deficiencies and for therapy of G6PD-mediated disorders.
Omens (1983)

53 OMENS It is there if You can read it: Runes in the barbed wire, Ciphers in knot-holes. And if you listen Then you will hear Mice moved into the larder, Squirrels under the eaves. And if you touch it You will know: Cat's-fur caught in The splinters of the fence. And if you follow, you Might get away, where there Is blood dried on the dead Leaves of the goldenrod. And if you do get away, Tell them. Do not Come here: first storm Of the last winter. J.B. GOODENOUGH ...
Pharmacokinetics of a water-soluble fullerene in rats (1996)

Fullerenes are the recently discovered third allotropic form of carbon. The biological activities of these compounds are being studied for various purposes. The bis(monosuccinimide) derivative of p p'-bis(2-amino-ethyl)-diphenyl-C60 (MSAD-C60) is a water-soluble fullerene derivative. MSAD-C60 has been shown to have antiviral activity against human immunodeficiency virus types 1 and 2 in vitro and to have virucidal and anti-human immunodeficiency virus protease activities. Moreover, MSAD-C60 has been shown to be well tolerated in mice after intraperitoneal administration. The purpose of the present study was to develop a high-performance liquid chromatographic analytical methodology for MSAD-C60 and to characterize the preclinical pharmacokinetics of the compound in rats. Following intravenous administration of the fullerene derivative at a dose of 15 mg/kg of body weight, the concentrations of MSAD-C60 in plasma declined either bi- or triexponentially. The mean terminal-phase half-life of MSAD-C60 was 6.8 +/- 1.1 h (mean +/- standard deviation). Binding studies indicated that the compound is greater than 99% bound to plasma proteins. The average total clearance of the compound was 0.19 +/- 0.06 liter/h/kg. Urine samples obtained 24 h after intravenous administration did not contain detectable levels of the compound, indicating the absence of a significant renal clearance mechanism. The steady-state volume of distribution of MSAD-C60 averaged 2.1 +/- 0.8 liters/kg, indicating that the compound distributes into tissues. At a dose of 15 mg/kg, MSAD-C60 appeared to be well tolerated. However, a dose of 25 mg/kg resulted in shortness of breath and violent movement of the rats, followed by death within 5 min of dosing. Further controlled toxicity studies are needed to fully evaluate the toxicity of the compound.
Abstract 1219: Integrative kinome exome sequencing and copy number profiling of ovarian clear cell carcinoma (2017)

Abstract Introduction: High stage ovarian clear cell carcinoma (OCCC) is less responsive to chemotherapy and has a worse prognosis than other ovarian cancer subtypes. The most frequently mutated genes in OCCC have been characterized in recent years. These include deleterious mutations in the tumor suppressor gene ARID1A, epigenetic silencing and deleterious mutations in the PI3K antagonist PTEN as well as activating mutations in the PI3K catalytic subunit PIK3CA. Yet, therapeutic strategies that utilize these genetic aberrations are lacking. In the present study, we aimed to identify and validate new kinase targets in OCCC. Methods: To determine new mutations and copy number gains and losses, kinome sequencing was performed on DNA isolated from tumor samples (n=124) and matched controls (n=47) and high-coverage SNP analysis was implemented for 109 of the collected OCCC tumor samples. Inhibitor sensitivity screening was performed on 17 OCCC cell lines to validate potential kinase targets, following in vivo validation in OCCC patient-derived xenografts (PDX). Results: Mutations in ARID1A, PIK3CA, PTEN, KRAS and TP53 corresponded to frequencies found in literature. Most identified mutations could be designated to the PI3K/Akt/mTOR and MAPK signal transduction pathway, and HER family of receptor tyrosine kinases. The PI3K pathway related genes PIK3R1, ERBB3 and AKT1 were significantly mutated in our dataset and not described in OCCC before. EGFR, ERBB2 and PIK3CA emerged as most frequently amplified kinases. Combining mutations and copy number alterations in these pathways, 91% of all tumors were affected. The highly positive staining of p-S6 (90% of OCCC tumors) indeed suggests high mTORC1/2 activity in these tumors. Inhibitor screening demonstrated subsets of cell lines to be sensitive to EGFR or ERBB2 inhibition. Furthermore, the vast majority of OCCC cell lines was susceptible to inhibition of PI3K and MAPK downstream target mTORC1/2 using AZD8055, which efficacy was further demonstrated in several OCCC PDX models. In contrast, mTORC1 inhibition alone was less effective. Conclusion: Most kinase mutations and copy number alterations in OCCC can be related to PI3K and MAPK pathway activation. In vitro and in vivo data suggest mTORC1/2 inhibition as a novel treatment strategy in OCCC. Combinations of EGFR or ERBB2 inhibition with mTORC1/2 targeted therapy can be envisioned for OCCC tumors with EGFR or ERBB2 alterations. Supported by a grant from the Dutch Cancer Foundation: RUG 2012-5477 Citation Format: J.j. Caumanns, G.b.a Wisman, K Berns, T. Tomar, R.s.n. Fehrmann, R Bernards, A.g.j. Van der Zee, S De Jong. Integrative kinome exome sequencing and copy number profiling of ovarian clear cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1219. doi:10.1158/1538-7445.AM2017-1219
Source and receiver deghosting by demigration‐based supervised learning (2022)

Abstract Deghosting of marine seismic data is an important and challenging step in the seismic processing flow. We describe a novel approach to train a supervised convolutional neural network to perform joint source and receiver deghosting of single‐component (hydrophone) data. The training dataset is generated by demigration of stacked depth migrated images into shot gathers with and without ghosts using the actual source and receiver locations from a real survey. To create demigrated data with ghosts, we need an estimate of the depth of the sources and receivers and the reflectivity of the sea surface. In the training process, we systematically perturbed these parameters to create variability in the ghost timing and amplitude and show that this makes the convolutional neural network more robust to variability in source/receiver depth, swells and sea surface reflectivity. We tested the new method on the Marmousi synthetic data and real North Sea field data and show that, in some respects, it performs better than a standard deterministic deghosting method based on least‐squares inversion in the τ‐p domain. On the synthetic data, we also demonstrate the robustness of the new method to variations in swells and sea‐surface reflectivity.
The MLL fusion partner AF10 binds GAS41, a protein that interacts with the human SWI/SNF complex (2002)

The AF10 gene encodes a putative transcription factor containing an N-terminal LAP/PHD zinc finger motif, a functional nuclear localization signal, an AT-hook domain, and a leucine zipper toward the C-terminus. AF10 is involved in 2 distinct chromosomal translocations associated with hematologic malignancy. The chimeric fusion proteins MLL/AF10 and CALM/AF10, resulting from the t(10;11)(p12;q23) and the t(10;11)(p12;q14), respectively, consistently retain the leucine zipper motif of AF10. This part of the C-terminal region was used as bait in a yeast 2 hybrid screening of a testis complementary DNA library. The leucine zipper interacted with GAS41, a protein previously identified as the product of an amplified gene in a glioblastoma. GAS41 shows significant homology to the Saccharomyces cerevisiae protein ANC1 and to the human MLL fusion partners AF9 and ENL. The interaction was confirmed in vivo. Furthermore, the study showed by coimmunoprecipitation that GAS41 interacts with INI1 (Integrase Interactor 1) and that INI1 was present in the AF10 immunoprecipitate. INI1 is the human homologue of the yeast SNF5 protein, a component of the SWI/SNF complex, which acts to remodel chromatin and to modulate transcription. The retention of the leucine zipper in the MLL and CALM fusions suggests that a key feature of these chimeric proteins may be their ability to interfere in normal gene regulation through interaction with the adenosine triphosphate-dependent chromatinremodeling complexes.
Metabolism of Pyruvate by the Early Human Embryo1 (1998)

Pyruvate is added to all media used for human in vitro fertilization and embryo culture, but its function(s) in the early embryo is unknown. We tested the possibility that pyruvate can act as an oxidizable energy source by measuring the consumption of pyruvate and oxygen by Day 2 and Day 3 human embryos, using microfluorometric techniques. Oxygen consumption (19.6 pmol/embryo per hour) could account for the oxidation of only 56% of the pyruvate consumed (13.9 pmol/embryo per hour). Oxygen was also consumed in the absence of exogenous substrates. Lactate appeared in the incubation medium with pyruvate (0.47 mM) as sole exogenous substrate at a rate of 12.1 pmol/embryo per hour, at a similar rate (10.85 pmol/embryo per hour) in the presence of 1 mM glucose and 0.47 mM pyruvate, and at 2.25 pmol/embryo per hour in the absence of exogenous substrates, suggesting that a high proportion of the pyruvate taken up by early human embryos is converted to lactate. Pyruvate uptake in the presence of UK5099, a pyruvate transport inhibitor, was reduced to 10% of control values, consistent with the presence of the monocarboxylate carrier in the human embryo plasma membrane.
Editorial Islet Cell Biology, Regeneration, and Transplantation (2012)

Copyright © 2012 A. N. Balamurugan et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Research studies centered on the biology, regeneration, and transplantation of islets continue to shed significant under-standing on the development of different forms of diabetes and provide further impetus for the quest to find a “cure.” Diabetes is a manifestation of an inadequate mass of insulin-producing pancreatic beta-cells.While type 1 is characterized by complete loss of beta-cells due to autoimmune attack on them, type 2 is characterized by a relative deficiency of beta-cells due to a decreased compensation for insulin resistance [1, 2]. Restoring beta-cell mass and reversing diabetes can be accomplished by two approaches: either by endogenous regeneration of beta-cells or transplantation of beta-cells
Improving the responsiveness of internet services with automatic cache placement (2009)

The backends of today's Internet services rely heavily on caching at various layers both to provide faster service to common requests and to reduce load on back-end components. Cache placement is especially challenging given the diversity of workloads handled by widely deployed Internet services. This paper presents TOOL, an analysis technique that automatically optimizes cache placement. Our experiments have shown that near-optimal cache placements vary significantly based on input distribution.
Best engineering practice for thermal characterization of stacked dice FPGA devices (2015)

This paper presents a couple of new methodologies regarding package characterization. An important shortcoming of the JEDEC methodology for single-die packages is that it does not account for the real-world scenario of a package's boundary condition. A new methodology is proposed to overcome this shortcoming by accounting for typical PCB conductivities and heatsink attachments to packages. The second methodology, presented in the paper, shows a better way to develop DELPHI-based boundary condition independent compact thermal models for 2.5D packages with multiple dies mounted on an interposer. This methodology, based on DELPHI-based techniques, accounts for the interaction between the multiple dies in a package. This is done by modifying the resistors generated from the optimization process. A number of verification cases show good fidelity of the compact thermal model to the detailed model.
A simple method for semi-random DNA amplicon fragmentation using the methylation-dependent restriction enzyme MspJI (2015)

The proposed method may be performed with standard laboratory equipment. Although the uniformity of coverage was slightly inferior to the Covaris physical shearing procedure, due to efficiencies of cost and labour, the method may be more suitable than existing approaches for implementation in large-scale sequencing activities, such as bacterial artificial chromosome (BAC)-based genome sequence assembly, pan-genomic studies and locus-targeted genotyping-by-sequencing.
Picosecond response of a superconducting hot-electron NbN photodetector (1998)

The ps optical response of ultrathin NbN photodetectors has been studied by electro-optic sampling. The detectors were fabricated by patterning ultrathin (3.5 nm thick) NbN films deposited on sapphire by reactive magnetron sputtering into either a 5×10 μm2 microbridge or 25 1 μm wide, 5 μm long strips connected in parallel. Both structures were placed at the center of a 4 mm long coplanar waveguide covered with Ti/Au. The photoresponse was studied at temperatures ranging from 2.15 K to 10 K, with the samples biased in the resistive (switched) state and illuminated with 100 fs wide laser pulses at 395 nm wavelength. At T=2.15 K, we obtained an approximately 100 ps wide transient, which corresponds to a NbN detector response time of 45 ps. The photoresponse can be attributed to the nonequilibrium electron heating effect, where the incident radiation increases the temperature of the electron subsystem, while the phonons act as the heat sink. The high-speed response of NbN devices makes them an excellent choice for an optoelectronic interface for superconducting digital circuits, as well as mixers for the terahertz regime. The multiple-strip detector showed a linear dependence on input optical power and a responsivity R=3.9 V/W.
Three-dimensional simulations of ultrasmall metal–oxide–semiconductor field-effect transistors: The role of the discrete impurities on the device terminal characteristics (2002)

We present results for the fluctuations in the threshold voltage and electron drift velocity in ultrasmall devices due to different numbers and distribution of impurity atoms in the device active region. We find that fluctuations in the threshold voltage VT are due to both the actual number and position of the dopant atoms. For the devices being considered, the correlation of the threshold voltage (average drift velocity) to the number of dopant atoms in a 10 nm range at various depths shows that the atoms in the top 15–20 nm (top 8 nm) beneath the channel have the most impact.
Supplementary Figure S3 from CMVpp65 Vaccine Enhances the Antitumor Efficacy of Adoptively Transferred CD19-Redirected CMV-Specific T Cells (2023)

&lt;p&gt;Supplementary Figure S3. Elevated cytokine levels in the serum of bi-specific T cell treated tumor bearing mice&lt;/p&gt;
TIME-LAPSE ELECTRICAL RESISTIVITY IMAGING OF PEATLAND GAS CONTENT INCORPORATING INDUCED POLARIZATION DATA (2014)

Time-lapse electrical resistivity imaging (ERI) studies are a popular means for monitoring and observing dynamic processes in the subsurface. While immensely informative, ERI inversion problems are ill-posed and rife with uncertainty. To stabilize the problem, the most common approach is to add a smoothness constraint that penalizes variation between adjacent model parameters. However, previous research has emphasized that discretization of significant features and zonal boundaries can immensely improve the quality of inversion results. While standard ERI data are primarily sensitive to current flow through pore fluid, induced polarization (IP) is a technique sensitive to both fluid and surface conduction pathways. Since these datasets can be collected simultaneously, they are often used to differentiate conductivity variation due to lithology versus changes due to pore fluid. Therefore, complex resistivity (combined ERI and IP) data have the potential to help identify structural boundaries for time-lapse ERI finite element meshes. Through synthetic experimentation, the effects of boundary discretization in a 3D time-lapse study monitoring changes in gas content within a basin feature are evaluated. This approach is applied to datasets from Caribou Bog, Maine through an initial characterization carried out through inversion of a complex resistivity dataset and calibrated using ground penetrating radar and direct coring results. In both cases, the improved characterization of the modeling domain better resolve areas of gas development.