gebhart/patrepeval huggingface dataset:
Abstract 3884: Stroke Subtypes in Hispanic Patients in the NINDS Stroke Genetics Network (SiGN): A Comparison of Two Classification Systems (2012)

Objectives: Identification of gene variants of stroke subtypes is important for the development of tailored ischemic stroke therapies among various ethnic groups. Valid and reliable determination of ischemic stroke subtype is essential for achieving this goal and to standardize a classification scheme across multi-center studies and different populations. Causative Classification System for Ischemic Stroke (CCS) is a novel computerized subclassification tool developed to improve reliability and accuracy of classifying stroke types. The CCS algorithm relies on both phenotypic and causative stroke variables. A Hispanic subset of the SiGN, an important and distinct target population with greater risk of certain stroke subtypes, was evaluated with Trial of Org 10172 in Acute Stroke Treatment (TOAST) and CCS and the agreement between the two classification systems was analyzed. Methods: Over 6000 subjects at 15 sites across US and Europe were enrolled, with TOAST and CCS locally adjudicated. Blood collection and central data quality control (10% central readjudication) were performed on all participants. A subset of Hispanics was analyzed for the purpose of this study and the agreement between the TOAST and CCS were assessed by kappa statistic. Findings: Hispanics (n=595, 10.9%) compared to non-Hispanics (n=5457) were more likely to be younger (63.7 vs. 64.0), male (55% vs. 46%) and have fewer of the traditional stroke risk factors HTN (54% vs. 64%), Afib (11% vs. 14%), DM(23% vs. 25%), CAD(16% vs. 20%) and smoking(19% vs. 22%). While the TOAST showed no differences between stroke subtypes for Hispanic vs. non-Hispanics, in CCS, Hispanics were classified with more of large vessel (22% vs. 20%), cardioembolic (37% vs. 30%) and small vessel strokes (13% vs. 9%) and fewer with undetermined etiology (28% vs. 40%) as compared to non-Hispanics. TOAST and CCS offered moderate correlation across all stroke types in Hispanics: kappa of 0.66 for large artery atherosclerosis, 0.58 for cardioembolic, and 0.58 for small artery occlusion. Conclusion: CCS offers a more sensitive and accurate system for subphenotyping of strokes in Hispanics who tended to have relatively fewer risk factors and unclassified strokes. Further studies correlating the two classification systems and their relation to genotyping data are warranted.
Low Oxygen and Inert Gas Processing of Foods (2006)

There are a lot of potential applications of low oxygen and
inert gas processing in food industry, for improvement of the product quality. It has widely been used in packaging and storage of foods. Inert gas processing of foods has been adopted to retain valuable nutrients by avoiding oxidation. Low oxygen or Inert gas processing reduces the oxidative losses in foods. It also retards the enzymatic browning by reducing the oxygen content. There is still a gap on the information on the effect of a few of the inert gases on spoilage and pathogenic microorganisms in the environment of fresh plant food products and the removal of residual gases and their effect on the browning enzyme system.
This indicates the need for further exploration in this area.The use of liquid nitrogen as a cryogen has a significant role in the food industry and has efficiently been adopted.
The selection of a standard STR panel for DNA profiling of the African elephant (Loxodonta africana) in Kenya (2014)

The African elephant (Loxodonta africana) population in Kenya is declining at an alarming rate due to habitat destruction, human-elephant conflicts and the current escalation of poaching for ivory. This study established a standard protocol for forensic analysis of L. africana and their products such as ivory. Three multiplex PCR panels consisting of 17 Short Tandem Repeat markers were selected from 40 markers using bioinformatics tools, amplification and polymorphism. Genotyping was successful and reproducible. This method is efficient, accurate and cost effective and has potential for application in conservation of L. africana.
Silicon(iv) complexes of octaaryl-substituted porphyrazines and corrolazines: influence of macrocycle contraction on spectral-luminescence, acid–base, and redox properties (2023)

The template cyclomerization of the iminoimide derivatives (obtained by the treatment of diarylfumarodinitriles with NH<sub>3</sub> in methanol containing catalytic amounts of dissolved Na) in the presence of SiCl<sub>4</sub> in pyridine leads to silicon(IV) octaarylporphyrazine complexes ((HO)<sub>2</sub>SiPzAr<sub>8</sub>, Ar = Ph, <sup><i>t</i></sup>BuPh) as a main reaction product. In the case of phenyl-substituted derivative, the formation of a distinctive Si(IV) complex as a byproduct was observed, which according to mass-spectroscopy measurement contains the macrocycle with five diphenylpyrrolic units. The treatment of bishydroxy complexes with tripropylchlorosilane in the presence of magnesium in pyridine leads to the formation of axially siloxylated porphyrazines (Pr<sub>3</sub>SiO)<sub>2</sub>SiPzAr<sub>8</sub>, followed by the reductive contraction of the macrocycle and formation of the corresponding corrolazine complexes (Pr<sub>3</sub>SiO)SiCzAr<sub>8</sub>. It is shown that the addition of acid (trifluoroacetic acid, TFA) facilitates the detachment of one siloxy group in (Pr<sub>3</sub>SiO)<sub>2</sub>SiPzAr<sub>8</sub> and is essential for its Pz → Cz transformation. In the presence of TFA, only one <i>meso</i>-nitrogen is protonated in the porphyrazine complexes (Pr<sub>3</sub>SiO)<sub>2</sub>SiPzAr<sub>8</sub> (stability constant of the protonated form p<i>K</i><sub>s1</sub> = -0.45 for Ar = Ph; p<i>K</i><sub>s1</sub> = 0.68 for Ar = <sup><i>t</i></sup>BuPh), while two consequent protonation stages are observed for the more basic corrolazine complex (Pr<sub>3</sub>SiO)SiCzPh<sub>8</sub> (p<i>K</i><sub>s1</sub> = 0.93, p<i>K</i><sub>s2</sub> = 0.45). Both types of Si(IV) complexes are poorly fluorescent (<i>Φ</i><sub>F</sub> < 0.07). The porphyrazine complexes have low ability to generate singlet oxygen (<i>Φ</i><sub>Δ</sub> < 0.15), whereas the corrolazine derivative (Pr<sub>3</sub>SiO)SiCzPh<sub>8</sub> is a very efficient photosensitizer (<i>Φ</i><sub>Δ</sub> = 0.76).
Study on new method and mechanism of low-temperature methanol synthesis (2011)

The methanol could be synthesized from the CO/CO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> /H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> on Cu/ZnO catalysts using alcohol solvent at 443 K and 3.0 Mpa. The activity of the catalyst with ZnO as carrier (Cu/ZnO) was the highest in all catalysts with Y <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> , La <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> , Al <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> , or MgO as carrier separately, and the 2-butanol as solvent exhibited the highest activity in this reaction. The studying results of the reaction mechanism show that at first adsorbed formate species were formed by adsorbing the CO/CO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> /H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> on Cu/ZnO catalyst, and then the 2-butyl formate was formed by the reaction of adsorbed formate species with 2-butanol, at last the 2-butyl formate is reduced by hydrogen atoms on Cu to form methanol. The 2-butanol used in this reaction not only significantly decreased the reaction temperature due to its promotional action, but also was not consumed due to its regeneration by hydrogenation of the 2-butyl formate, acting like a catalytic solvent.
Lateral blow-out failure of headed studs near a free edge (1991)

Pullout tests with headed studs placed near a free edge have been carried out. In most of the tests blow-out failure occurred. On the basis of this and other available test results an empirical equation for calculating the failure load was derived. The equation takes into account the influence of the edge distance, the concrete strength and the load bearing area. The equation for calculating the failure load shows good agreement with the test results. The equation for calculating the critical edge distance at which the failure mode changes to steel rupture or to concrete cone failure is given. The values for critical edge distance are different from the values in ACI 349, Appendix B, because of the ACI 349 overestimates the concrete capacity for large edge distances.
PTU-019 Nasal or standard endoscopy (nose) for diagnosis of Barrett's oesophagus – efficacy and patient tolerance (2010)

<h3>Introduction</h3> In order to detect all cases of Barrett9s oesophagus (BE) in the population, with the aim of reducing adenocarcinoma associated mortality, screening needs to be considered. Unsedated transnasal endoscopy (TNE) can potentially offer a safer and less expensive alternative to conventional sedated endoscopy (CE) for detecting BE. <h3>Aims</h3> (1) To evaluate the sensitivity and specificity of TNE in diagnosing BE compared with CE. (2) To assess patient acceptability of TNE for a future multicentre screening trial. <h3>Methods</h3> Patients with known BE under surveillance and those referred for routine endoscopy for other reasons underwent both TNE and CE in a randomised cross-over design. TNE findings of endoscopic BE, biopsy size and presence of intestinal metaplasia (IM) were compared against CE, which was used as gold standard. Pre and post endoscopy short-form spielberger state-trait questionnaires (SF6), a visual analogue scale and a single question addressing preference for endoscopy type were used to measure patient acceptability of the procedures. <h3>Results</h3> Of 57 patients randomised, 50 completed the study. All 22 BE cases with columnar lined epithelium (CLE) on CE were correctly diagnosed by TNE. Although the biopsy size of TNE was significantly smaller compared to CE (mean size 2.59 vs 4.74 p&lt;0.0001), it detected an equal number of IM cases and there was one case of low grade dysplasia which interestingly was not picked up by CE. Abstract 019 shows sensitivity, specificity and diagnostic accuracy (including Pearson-Clopper CI) for diagnosing BE and IM using TNE compared with CE as the gold standard. The mean difference between the two procedures in determining the length of BE was 0.02. The 95% Bland and Altman limits of agreement was between −2.08 and 2.13 with 49 cases (98%) falling within the pre-determined level of agreement of ±1.5 cm. The mean pre and post procedure anxiety score for TNE (13.3 vs 14.0) and CE (13.2 vs 13.5) were not significantly different (p=0.15). The post endoscopy experience of TNE was comparable to CE (mean 5.0 vs 4.9, p=0.77). <h3>Conclusion</h3> TNE is accurate in diagnosing BE and detecting IM. Despite the smaller biopsy size, it detected an equal number of IM cases and showed potential to detect dysplasia. It was well tolerated and preferred by patients and may be an efficient screening method for BE.
Hamstring contractures in children with spastic cerebral palsy result from a stiffer extracellular matrix and increased in vivo sarcomere length. (2011)

Non-technical summary
Muscle spasticity, due to an upper motoneuron lesion, often leads to muscle contractures that limit range of motion and cause increased muscle stiffness. However, the elements responsible for this muscle adaption are unknown. Here we show that muscle tissue is stiffer in contracture compared to age-matched children, implicating the extracellular matrix (ECM). However, titin, the major load-bearing protein within muscle fibres, is not altered in contracture, and individual fibre stiffness is unaltered. Increased ECM stiffness is even more functionally significant given our finding of long in vivo sarcomeres which leads to much larger in vivo forces in muscle contracture. These results may lead to novel therapeutics for treating spastic muscle contracture.
Cyclopentasilane-Fused Hexasilabenzvalene (2013)

Cyclopentasilane-fused hexasilabenzvalene 1 was synthesized by the reduction of tetrachlorocyclopentasilane 6 in 19% yield as a green powder. The molecular structure and properties of 1 were studied by spectroscopic and X-ray crystallographic analyses. Theoretical calculations of the model and real molecules of 1 and their structural isomers 12–16 suggest that the linkage of the central hexasilabenzvalene moiety with trisilane chains and the introduction of tert-butyl groups affect their relative energies.
The cytoplasmic prolyl-tRNA synthetase of the malaria parasite is a dual-stage target of febrifugine and its analogs (2015)

The emergence of drug resistance is a major limitation of current antimalarials. The discovery of new druggable targets and pathways including those that are critical for multiple life cycle stages of the malaria parasite is a major goal for developing next-generation antimalarial drugs. Using an integrated chemogenomics approach that combined drug resistance selection, whole-genome sequencing, and an orthogonal yeast model, we demonstrate that the cytoplasmic prolyl–tRNA (transfer RNA) synthetase (PfcPRS) of the malaria parasite Plasmodium falciparum is a biochemical and functional target of febrifugine and its synthetic derivative halofuginone. Febrifugine is the active principle of a traditional Chinese herbal remedy for malaria. We show that treatment with febrifugine derivatives activated the amino acid starvation response in both P. falciparum and a transgenic yeast strain expressing PfcPRS. We further demonstrate in the Plasmodium berghei mouse model of malaria that halofuginol, a new halofuginone analog that we developed, is active against both liver and asexual blood stages of the malaria parasite. Halofuginol, unlike halofuginone and febrifugine, is well tolerated at efficacious doses and represents a promising lead for the development of dual-stage next-generation antimalarials.
NMR study on sulfonation of internal olefins (1991)

Abstract Terminal olefins can be converted into the corresponding sulfonates by sulfonation with SO 3 followed by hydrolysis, the products are used as detergent ingredients. Although internal olefins were also expected to be good feed stocks, it was difficult to convert them into the corresponding sulfonates with as good of a yield as that of terminal olefins under the same synthesis conditions. Our studies have been carried out in order to clarify the reason for poorer conversion of the internal olefins. It was found by a nuclear magnetic resonance spectroscopic study that the major components of the sulfonated intermediate of internal olefins were β ‐sultones, the amounts of which were usually very small in sulfonated terminal olefins. A portion of these β ‐sultones was desulfonated, depending on temperature, to the original olefins and the corresponding sulfate salts during alkaline hydrolysis. The prevention of desulfonation of the β ‐sultones in the hydrolysis process was one of the most important aspects for the production of internal olefin sulfonates. Finally, by keeping the hydrolysis temperature below 35°C, the conversion of internal olefins into sulfonates was achieved with the same yield as that of conventional terminal olefins.
Simulation of the dynamics of electron transfer reactions in polar solvents: Semiclassical trajectories and dispersed polaron approaches (1986)

Simulation methods for exploring the microscopic aspects of electron transfer (ET) reactions are developed. For the high temperature limit, where anharmonicity effects are crucial, we develop a semiclassical trajectory (ST) method. This method treats the reaction by considering the time dependence of the electronic energy gap along the classical trajectories of the solvent molecules. The ST approach, which appears as an ad hoc approach, might be at present the most rigorous practical models for simulating ET reactions. That is, this method reproduces the results of the quantum mechanical harmonic test case in the high temperature statistical limit. More importantly, for anharmonic systems it provides a rate constant which depends on the proper activation free energy; this dependence cannot be evaluated by any of the current quantum mechanical methods. For the low temperature range we develop a ‘‘dispersed polaron’’ model that uses the Fourier transform of the microscopic energy gap to evaluate the harmonic Franck–Condon factors of the system. These Franck–Condon factors are then used to evaluate the quantum mechanical harmonic rate constant. The potential of our approach is outlined by considering its implementation in studies of several key problems. This includes: (i) Studies of the effect of solvent dynamics and the role of dielectric relaxation times. (ii) Studies of the actual microscopic activation free energy. (iii) Exploration of the role of vibronic channels in the inverted region. (iv) Transition between the adiabatic and diabatic limits.
Energetics of isometric contractions as a function of muscle temperature (1983)

The energetic cost of generating isometric force in isolated frog muscle was examined at 10, 20, and 30 degrees C. Recovery O2 consumption (delta O2) and recovery lactate production (delta Lact) were measured under conditions in which O2 was not limiting metabolism. Both increased linearly with the force-time integral (integral of Fdt) generated by the muscle. The slopes of the regression equations for both delta O2 and delta Lact as a function of integral of Fdt increased with increasing temperature with a temperature coefficient (Q10) near 3. Total high-energy phosphate resynthesis from recovery metabolism was calculated by scaling the delta O2 regression equation and the delta Lact regression equation into equivalent ATP units and summing them. This total recovery metabolism was modeled as the sum of two components, a "cost of maintaining force" (slope of the equation) and a saturable "start up cost" (intercept of the equation). The cost of maintaining force increased with temperature with a Q10 near 3 over the whole temperature range, whereas the start up cost was nearly independent of temperature between 0 and 20 degrees C and fell to near zero at 30 degrees C. Delta O2 measurements from a series of tetani given in rapid succession showed that for contractions subsequent to the first, no start up cost was incurred and that the "cost of generating force" for these contractions was equal to the slope of the regression line for single tetani. The practical consequence of these facts is that, in series of tetani, the cost of generating force increases with a Q10 of 3.
A Route from Darkness to Light: Emergence and Evolution of Luciferase Activity in AMP-CoA-Ligases Inferred from a Mealworm Luciferase-like Enzyme (2013)

The origin of luciferases and of bioluminescence is enigmatic. In beetles, luciferases seem to have evolved from AMP-CoA-ligases. How the new oxygenase luminogenic function originated from AMP-ligases leading to luciferases is one of the most challenging mysteries of bioluminescence. Comparison of the cloned luciferase-like enzyme from the nonluminescent Zophobas morio mealworm and beetle luciferases showed that the oxygenase activity may have emerged as a stereoselective oxidative drift with d-luciferin, a substrate that cannot be easily thioesterified to CoA as in the case of the l-isomer. While the overall kcat displayed by beetle luciferases is orders of magnitude greater than that of the luciferase-like enzyme, the respective oxidation rates and quantum yields of bioluminescence are roughly similar, suggesting that the rate constant of the AMP-ligase activity exerted on the new d-luciferin substrate in beetle protoluciferases was the main enzymatic property that suffered optimization during the evolution of luciferases. The luciferase-like enzyme and luciferases boost the rate of luciferyl-adenylate chemiluminescent oxidation by factors of 10(6) and 10(7), respectively, as compared to the substrate spontaneous oxidation in buffer. A similar enhancement of luciferyl-adenylate chemiluminescence is provided by nucleophilic aprotic solvents, implying that the peptide bonds in the luciferin binding site of beetle luciferase could provide a similar catalytically favorable environment. These data suggest that the luciferase-like enzyme and other similar AMP-ligases are potential alternative oxygenases. Site-directed mutagenesis studies of the luciferase-like enzyme and the red light-producing luciferase of Phrixotrix hirtus railroadworm confirm here a critical role for T/S345 in luciferase function. Mutations such as I327T/S in the luciferase-like enzyme, which simultaneously increases luciferase activity and promotes blue shifts in the emission spectrum, could have been critical for evolving functional bioluminescence from red-emitting protoluciferases. Through the combination of I327T/S mutations and N-terminal fusion, the luminescence activity of this enzyme was increased to visible levels, with the development of a totally new orange-emitting luciferase. These results open the possibility of engineering luciferase activity in a set of AMP-CoA-ligases.
Effect of Phosphatidylserine Content on the Partition Coefficients of Diazepam and Flurazepam between Phosphatidylcholine-Phosphatidylserine Bilayer of Small Unilamellar Vesicles and Water Studied by Second Derivative Spectrophotometry. (2002)

The affinity of the psychotropic benzodiazepine drugs diazepam (DZ) and flurazepam (FZ) to phosphatidylserine (PS) was examined since PS is abundantly contained in brain membranes. The effect of PS content on the partition coefficients (K(p)s) of these drugs between phosphatidylcholine (PC)-PS bilayer membranes of small unilamellar vesicles (SUV) and water was measured using second derivative spectrophotometry. The second derivative spectra of DZ and FZ measured in the solutions containing various amounts of PC-PS SUV clearly showed derivative isosbestic points and a distinct derivative intensity change depending on the amount of the SUV added. The derivative intensity differences (AD) of the drugs before and after addition of the SUV suspension were measured at a specific wavelength. Using the AD values, the Kp values were calculated and obtained with relative standard deviation of below 10%. The Kp values of both drugs increased according to the PS content in the PS-PC bilayer membranes of the SUV proving that both have higher affinity to the PC-PS bilayer membranes than to PC membranes. The effect was much larger for FZ, i.e., the Kp value of FZ at 30 mol% PS content increased to about five times the value for the PC SUV. This can be explained by the fact that at the experimental pH of 7.4, 80% of FZ molecules are in a cationic form (pKa=8.1), so that these molecules are highly accessible to the negatively charged PS molecules. The results support the rapid and high distribution of DZ and FZ in the central nervous system after their administration.
Membrane-protein-hydration interaction of alpha-synuclein with anionic vesicles in solution probed via angle-resolved second harmonic scattering (2019)

LBP
A Binary Deoxyribozyme for Nucleic Acid Analysis (2007)

A binary star is born. Two unmodified DNA strands were found to form a catalytically active core upon hybridization to abutting positions of a DNA analyte (see figure). The DNAzyme cleaved a fluorophore- and quencher-labeled substrate; this resulted in increased fluorescence of the solution.