gebhart/patrepeval huggingface dataset:
Biochemical and Structural Characterization of MycCI, a Versatile P450 Biocatalyst from the Mycinamicin Biosynthetic Pathway (2016)

Cytochrome P450 monooxygenases (P450s) are some of nature's most ubiquitous and versatile enzymes for performing oxidative metabolic transformations. Their unmatched ability to selectively functionalize inert C-H bonds has led to their increasing employment in academic and industrial settings for the production of fine and commodity chemicals. Many of the most interesting and potentially biocatalytically useful P450s come from microorganisms, where they catalyze key tailoring reactions in natural product biosynthetic pathways. While most of these enzymes act on structurally complex pathway intermediates with high selectivity, they often exhibit narrow substrate scope, thus limiting their broader application. In the present study, we investigated the reactivity of the P450 MycCI from the mycinamicin biosynthetic pathway toward a variety of macrocyclic compounds and discovered that the enzyme exhibits appreciable activity on several 16-membered ring macrolactones independent of their glycosylation state. These results were corroborated by performing equilibrium substrate binding experiments, steady-state kinetics studies, and X-ray crystallographic analysis of MycCI bound to its native substrate mycinamicin VIII. We also characterized TylHI, a homologous P450 from the tylosin pathway, and showed that its substrate scope is severely restricted compared to MycCI. Thus, the ability of the latter to hydroxylate both macrocyclic aglycones and macrolides sets it apart from related biosynthetic P450s and highlights its potential for developing novel P450 biocatalysts with broad substrate scope and high regioselectivity.
Rapid thermal processing of steel using high energy electron beams (1993)

High energy electron beams (HEEBs) with megavolt energies represent a new generation of charged particle beams that rapidly deposit up to several hundred joules/pulse over areas on the order of a few square millimeters to 100s of square centimeters. These pulsed beams have energies in the 1 to 10 MeV range, which enables the electrons to deposit large amounts of energy deeply into the material being processed, and these beams have short pulse durations (50 ns) that can heat materials at rates as high as 10{sup 10} {degrees}C/s for a 1000 {degree}C temperature rise in the material. Lower heating rates, on the order of 10{sup 4} {degrees}C/s, can be produced by reducing the energy per pulse and distributing the total required energy over a series of sub-ms pulses, at pulse repetition frequencies (PRFs) up to several kHz. This paper presents results from materials processing experiments performed on steel with a 6 MeV electron beam, analyzes these results using a Monte Carlo transport code, and presents a first-order predictive method for estimating the peak energy deposition, temperature, and heating rate for HEEB processed steel.
Temperature Effect on Electronic Structure of High-Temperature Sensing Materials (2021)

Presented by NETL at ACS Fall Meeting 08/19
DOP058 Pharmacokinetic and pharmacodynamic relationship and immunogenicity of vedolizumab in adults with inflammatory bowel disease: Additional results from the GEMINI 1 and 2 studies (2014)

Background: There is increasing evidence on the role of low trough levels and the development of anti-TNF-a antibodies for the occurrence of lack/loss of response to Infliximab (IFX) therapy in patients with Crohn's Disease (CD). Therefore, several recent papers and guidelines suggested the need for dosing IFX concentrations and anti-IFX antibodies in order to treat better CD patients. To date, there are limited data on the role of adalimumab (ADA) through levels and anti-ADA antibodies (AAA) for the management of CD patients. Aim: We assessed the role of AAA on ADA trough levels, TNF-a concentrations, PCR value and clinical outcome. Methods: In this prospective observational cohort study, performed at a single tertiary referral center, 23 [14M/9F; mean age 41 (range 21 66)] infliximab-nave patients with CD achieving disease remission and in maintenance treatment with ADA were included in a follow-up program. Blood samples were drawn at standardized time points (i.e. at 6, 12, 18, 24 months and in case of relapse) just before ADA injection. Trough serum concentration and antibodies against ADA were measured using an homogenous mobility shift assay (HMSA; Prometheus Lab, San Diego, United States). Blood samples were considered positive for they presence if AAA were >1.7 U/mL and for ADA through levels if they levels were more than >5 mg/ml. Disease activity was assessed at the same points by means of routine biochemistry and the Harvey Bradshaw Index (HBI, remission <5, mild disease 5 7, moderate disease 8 16, severe disease >16). Results: We have data from 189 blood samples. AAA were observed in 42/189 (22.2%) samples, and 16/42 (38.1%) had levels of AAA >1.7 U/mL. ADA through levels were found in 183/189 (96.8%) samples, and 168/183 (91.8%) had a value of drug levels >5 mg/ml. Overall, 5/23 (21.7%) patients had AAA and 22/23 (95.6%) were positive for ADA levels. Blood samples with AAA had lower ADA trough levels [7.54 (0 26.49) vs. 9.45 (0.14 23.62); p = 0.002] and higher TNF-a concentrations [5.9 (4.1 11.5) vs. 3.6 (0 27.2); p = 0.0007] than blood samples without evidence of AAA. Moreover, patients with blood samples positive for AAA reported HBI values higher compared to patients without evidence of AAA [10 (3 17) vs. 5 (2 17); p < 0.0001]. Finally, no differences were found in terms of mean PCR values between patients with AAA and those without [8.1 (3 76.4) vs. 5.2 (2.6 56); p = 0.39]. Conclusions: Development and presence of AAA influence ADA trough levels and TNF-a concentrations in CD patients during maintenance treatment with ADA, thus favoring clinical relapse as demonstrated by the increased values of HBI scores.
Selective Diffusion of C8 Aromatics in a 10 and 12 MR Zeolite. A Molecular Dynamics Study (1998)

Molecular dynamics simulations employing a flexible framework are used to simulate the diffusion of o- and p-xylene in purely siliceous zeolite CIT-1. The simulations are performed at 500 K, investigating two loadings (corresponding to 1 molecule/unit cell and 0.25 molecule/unit cell) for the ortho isomer and one loading (0.25 molecule/unit cell) for the para isomer. For the former system the diffusion coefficient decreases from 7.79 × 10-6 cm2/s for the lower to 3.56 × 10-6 cm2/s for the higher loading. The diffusion coefficient for the para isomer (25.18 × 10-6 cm2/s) is substantially greater. Graphical analyses reveal a jump diffusion mechanism, which in the case of the ortho isomer takes place in the 12 MR channels of the structure, while for the para isomer, incursions into the 10 MR channel are observed. The results of the MD simulations are complemented and reinforced by calculations of the activation energies for the diffusion of the two isomers in the two channels. Diffusivity measurements of both isomers in B-CIT-1 (Si/Al = 35) by FTIR have also been carried out in order to compare the values obtained theoretically and experimentally.
Automated electron tomography: from data collection to image processing (1995)

Electron tomography is a technique where many projections of an object are collected from the transmission electron microscope (TEM), and are then used to reconstruct the object in its entirety, allowing internal structure to be viewed. As vital as is the 3-D structural information and with no other 3-D imaging technique to compete in its resolution range, electron tomography of amorphous structures has been exercised only sporadically over the last ten years. Its general lack of popularity can be attributed to the tediousness of the entire process starting from the data collection, image processing for reconstruction, and extending to the 3-D image analysis. We have been investing effort to automate all aspects of electron tomography. Our systems of data collection and tomographic image processing will be briefly described. To date, we have developed a second generation automated data collection system based on an SGI workstation (Fig. 1) (The previous version used a micro VAX). The computer takes full control of the microscope operations with its graphical menu driven environment. This is made possible by the direct digital recording of images using the CCD camera.
Total Synthesis and Determination of the Absolute Configuration of Rishirilide B: Exploitation of Subtle Effects to Control the Sense of Cycloaddition of o‐Quinodimethides. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
QUIC Multipath Negotiation Option (1998)

The initial version of QUIC provides support for path migration. In
this draft, we argue that there is a very small distance between
supporting path migration and supporting simulatneous traffic on
multipath. Instead of using an implicit algorithm to discard unused
paths, we propose a simple option to allow explicit management of
active and inactive paths. Once paths are explicitly managed, pretty
much all other requirements for multipath support can be met by
appropriate algorithms for scheduling transmissions on specific paths.
These algorithms can be implemented on the sender side, and do not
require specific extensions, except maybe a measurement of one way
delays.
LiFePO4- Li-ion Polymer TechnologyFor Cleaner Transportation (2006)

Abstract not Available.
Production of single-walled carbon nanotube grids (2015)

A method of forming a nanotube grid includes placing a plurality of catalyst nanoparticles on a grid framework, contacting the catalyst nanoparticles with a gas mixture that includes hydrogen and a carbon source in a reaction chamber, forming an activated gas from the gas mixture, heating the grid framework and activated gas, and controlling a growth time to generate a single-wall carbon nanotube array radially about the grid framework. A filter membrane may be produced by this method.
High performance spatial data mining: scalable methods for spatial autoregression (2005)

Explosive growth in the size of spatial databases has highlighted the need for spatial data mining techniques to mine the interesting but implicit spatial patterns within these large databases. This thesis deals with reducing the computational complexity of the exact and approximate spatial autoregression (SAR) model solutions. Estimation of the parameters of the SAR model using Maximum Likelihood (ML) theory is computationally very expensive because of the need to compute the logarithm of the determinant (log-det) of a large matrix in the log-likelihood function. 
The first part of the thesis introduces theory on SAR model solutions. The second part applies parallel processing techniques to the exact SAR model solutions. We proposed parallel formulations of the SAR model parameter estimation procedure based on ML theory using data parallelism with load-balancing techniques. 
Although this parallel implementation showed scalability up to eight processors, the exact SAR model solution still suffers from high computational complexity and memory requirements. These limitations have led us to investigate serial and parallel approximate solutions for SAR model parameter estimation. In the third part of the thesis, we present two candidate approximate-semi-sparse solutions of the SAR model based on Taylor's Series expansion and Chebyshev Polynomials. We showed that the differences between exact and approximate SAR parameter estimates have no significant effect on the prediction accuracy. 
We developed a new ML based approximate SAR model solution and its variants in the next part of the thesis. The new approximate SAR model solution is called the Gauss-Lanczos approximated SAR model solution. We algebraically rank the error of the Chebyshev Polynomial approximation, Taylor's Series approximation and the Gauss-Lanczos approximation to the solution of the SAR model and its variants. In other words, we established a novel relationship between the error in the log-det term; which is the approximated term in the concentrated log-likelihood function and the error in estimating the SAR parameter ρ for all of the approximate model solutions. 
In the last part of the thesis, we present a faster, scalable and novel prediction and estimation technique for the exact SAR model solution (NORTHSTAR). We provide a proof of the correctness of ML based SAR model solutions by showing the objective function to be uni-modular.
Inductive Links for 3D Stacked Chip-to-Chip Communication (2019)

This paper focusses on an experimental inductive link study based on S-parameter measurements up to 67 GHz for 3D stacked chip to chip communication. This is complemented by a calibrated HFSS model for coupling between two chips that is then extended to stacks with up to eight chips. This approach allows for a complete analysis of the inductive link mechanisms between stacked chips and the impact of different parameters. Moreover, a circuit level assessment of the inductive link for a transmitter circuit has been performed using FinFET technology.
Preparative Synthesis via Continuous Flow of 4,4,5,5-Tetramethyl-2-(3-trimethylsilyl-2-propynyl)-1,3,2-dioxaborolane: A General Propargylation Reagent (2011)

A scalable process for the preparation of 4,4,5,5-tetramethyl-2-(3-trimethylsilyl-2-propynyl)-1,3,2-dioxaborolane from trimethylsilylpropyne, isopropyl pinacol borate, and n-butyllithium is described. Problems associated with implementing a typical aqueous workup and batch process into production due to borolane “ate” equilibration and protonolysis are presented. To address these issues, a continuous-flow and distillation process was developed which efficiently produced 297 kg of the key propargylation reagent.
Global differences in heart failure with preserved ejection fraction: the paragon-hf trial (2020)

Abstract Background Heart failure with preserved ejection fraction (HFpEF) is a global public health problem with important regional differences. We investigated these differences in the PARAGON-HF trial, the largest, most inclusive global HFpEF trial. Methods We studied differences in clinical characteristics, outcomes and regional treatment effects of Sacubitril/Valsartan in 4796 patients with HFpEF from the PARAGON-HF trial, grouped according to geographic region. Results Regional differences in patient characteristics and comorbidities were observed (Figure 1): patients from Western Europe were oldest (75±7 years) with the highest prevalence of atrial fibrillation (36%); Central/Eastern European patients were youngest (71±8 years) with the highest prevalence of coronary artery disease (CAD, 49%); North American patients had the highest prevalence of obesity (64%) with metabolic syndrome; Latin American patients were youngest and had a high prevalence of obesity (53%); Asia-Pacific patients had a high prevalence of diabetes (44%) despite low prevalence of obesity (26%). Rates of the primary composite endpoint of total hospitalizations for HF and death from cardiovascular causes was lowest in patients from Central Europe (9 per 100 patient years) and highest in patients from North America (28 per 100 patient years), which was primarily driven by a greater number of total hospitalizations for HF and independent of confounders. In the total population, sacubitril–valsartan did not result in a significantly lower rate of total hospitalizations for heart failure and death from cardiovascular causes with no significant heterogeneity in treatment response to sacubitril-valsartan across regions. Conclusion This first report on regional differences in the largest prospective global trial in HFpEF suggests substantial regional heterogeneity with respect to phenotype, outcomes and quality of life. Figure 1 Funding Acknowledgement Type of funding source: Private company. Main funding source(s): Study funded by Novartis
Molecular Iodine Initiates Hydroborations of Alkenes with N-Heterocyclic Carbene Boranes (2013)

The hydroboration of alkenes of diverse structural types by assorted N-heterocyclic carbene boranes can be accomplished by addition of 5-10% diiodine. For example, reaction of 1,3-dimethylimidazol-2-ylidene borane (diMe-Imd-BH3) with 10% I2 followed by addition of 2,3-dimethyl-2-butene provided the corresponding thexyl NHC-borane (diMe-Imd-BH2thexyl) in 75% yield. This and related monohydroboration products are stable to chromatography and storage. The scope of the new reaction is described, and the mechanism is probed by (11)B NMR experiments.
Thermal Tuning of Surface Plasmon Polaritons Using Liquid Crystals (2013)

A thermally controlled plasmonic substrate supporting surface plasmon polaritons in contact with a liquid crystal medium is presented. The platform offers a spectral tuning range ∼18.7 nm by controlling the refractive index of the liquid crystal medium within the nematic phase in a temperature range of 18 °C. The abrupt transition between nematic and isotropic phases also enables a spectral tuning as large as 12 nm with only ∼1 °C. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Measurements of prompt charm production cross-sections in pp collisions at s = 13 $$ \sqrt{s}=13 $$ TeV (2016)

Production cross-sections of prompt charm mesons are measured with the first data from pp collisions at the LHC at a centre-of-mass energy of 13 TeV. The data sample corresponds to an integrated luminosity of 4.98 0.19 pb -1 collected by the LHCb experiment. The production cross-sections of D 0 , D + , D + s , and D * + mesons are measured in bins of charm meson transverse momentum, p T , and rapidity, y, and cover the range 0 < p T < 15 GeV/c and 2.0 < y < 4.5. The inclusive cross-sections for the four mesons, including charge conjugation, within the range of 1 < p T < 8 GeV/c are found to be
Many disease-associated variants of hTERT retain high telomerase enzymatic activity (2013)

Mutations in the gene for telomerase reverse transcriptase (hTERT) are associated with diseases including dyskeratosis congenita, aplastic anemia, pulmonary fibrosis and cancer. Understanding the molecular basis of these telomerase-associated diseases requires dependable quantitative measurements of telomerase enzyme activity. Furthermore, recent findings that the human POT1-TPP1 chromosome end-binding protein complex stimulates telomerase activity and processivity provide incentive for testing variant telomerases in the presence of these factors. In the present work, we compare multiple disease-associated hTERT variants reconstituted with the RNA subunit hTR in two systems (rabbit reticulocyte lysates and human cell lines) with respect to telomerase enzymatic activity, processivity and activation by telomere proteins. Surprisingly, many of the previously reported disease-associated hTERT alleles give near-normal telomerase enzyme activity. It is possible that a small deficit in telomerase activity is sufficient to cause telomere shortening over many years. Alternatively, mutations may perturb functions such as the recruitment of telomerase to telomeres, which are essential in vivo but not revealed by simple enzyme assays.
Effect of a Boron Additive on the Microstructure and Dielectric Properties of BaTiO<sub>3</sub> Thin Films Formed by Nanocrystal Deposition (2013)

Highly crystallized BaTiO 3 thin films were fabricated by a nanocrystal sintering process. Boron alkoxide was introduced into a slurry of Mn-doped BaTiO 3 nanocrystals with particle sizes of 5-7 nm. The deposited nanocrystal film on a (111)-oriented Pt/TiO 2 /Al 2 O 3 substrate was sintered at a low temperature of 800 °C and the obtained film had highly densified and oriented microstructures. We found that the boron additive enhanced the grain growth of nanoparticles and as a result the dielectric constant of the thin film increased to 1100 at 10 kHz, which is much higher than that of undoped BaTiO 3 thin films.
The Development of High Temperature Thermoplastic Composite Materials for Additive Manufactured Autoclave Tooling (2017)

In this work, ORNL and Techmer investigated and screened different high temperature thermoplastic reinforced materials to fabricate composite molds for autoclave processes using Additive Manufacturing (AM) techniques. This project directly led to the development and commercial release of two printable, high temperature composite materials available through Techmer PM. These new materials are targeted for high temperature tooling made via large scale additive manufacturing.
Diphosphopyridine nucleotide: a cofactor for the polynucleotide-joining enzyme from Escherichia coli. (1967)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Structure—Activity Relationships of a Novel Class of Endothelin Receptor Selective Antagonists; 6‐Carboxy‐2‐isopropylamino‐5,7‐diarylcyclopenteno[1,2‐b]pyridines. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Collisional Excitation (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
Efficient I/O for computational grid applications. (2003)

High-performance computing increasingly occurs on “computational grids” composed of heterogeneous and geographically distributed systems of computers, networks, and storage devices that collectively act as a single “virtual” computer. A key challenge in this environment is to provide efficient access to data distributed across remote data servers. This dissertation explores some of the issues associated with I/O for wide-area distributed computing and describes an I/O system, called Armada, with the following features: a framework to allow application and dataset providers to flexibly compose graphs of processing modules that describe the distribution, application interfaces, and processing required of the dataset before or after computation; an algorithm to restructure application graphs to increase parallelism and to improve network performance in a wide-area network; and a hierarchical graph-partitioning scheme that deploys components of the application graph in a way that is both beneficial to the application and sensitive to the administrative policies of the different administrative domains. Experiments show that applications using Armada perform well in both low- and high-bandwidth environments, and that our approach does an exceptional job of hiding the network latency inherent in grid computing.