gebhart/patrepeval huggingface dataset:
Further insights into peroxisomal lipid breakdown via α- and β-oxidation (2001)

Mammalian peroxisomes degrade fatty carboxylates via two pathways, beta-oxidation and, as shown more recently, alpha-oxidation. The latter process consists of an activation step, followed by a hydroxylation at position 2 and cleavage of the 2-hydroxyacyl-CoA, generating formyl-CoA (precursor of formate/CO(2)) and, in case of phytanic acid as substrate, pristanal (precursor of pristanic acid). The stereochemistry of the overall pathway, cofactor requirements and substrate specificity of the hydroxylase and the cleavage enzyme, which is homologous with bacterial oxalyl-CoA decarboxylases, will be discussed. With regard to beta-oxidation, peroxisomes contain different acyl-CoA oxidases, multifunctional proteins and thiolases. Based on substrate spectra and stereospecificities of these enzymes, a model was proposed whereby straight chain and branched compounds are degraded by separate pathways. The biochemical findings in mice lacking the D-specific multifunctional protein, however, do not fully support this model. These animals, together with the Pex5(-/-) mice, might be useful to pinpoint the pathological factors contributing to the brain abnormalities in Zellweger patients. Apparently, the deficit in docosahexaenoic acid, presumably formed via peroxisomal beta-oxidation, is not the major cause.
Use of Carbonate and Alkali To Eliminate Escherichia coli from Dairy Cattle Manure (2000)

A procedure to eliminate Escherichia coli in dairy cattle manure was developed. E. coli persisted in fresh manure and farm storage tanks, and viable counts ranged from 105 to 108/g. If the feces to urine ratio of fresh manure was decreased from 2.2 to 1, E. coli did not persist for ≥10 days (<10 viable cells/g), and it appeared that the urine was killing E. coli. Fecal urease contamination produced CO2, and 16% was trapped as carbonate. When urine pH was decreased, antimicrobial effect was lost, even if the pH was readjusted to 8.5. When E. coli K-12 and O157:H7 were treated with Na2CO3 (100 mM, pH 8.5, 24 h), viable cells were not detected. The E. coli count of manure (feces to urine ratio of 2.2:1) was decreased by Na2CO3 addition (8 g/kg), but pH sometimes declined and carbonate was lost. When NaOH was included (2 g/kg), Na2CO3 additions could be decreased (4 g/kg), and treatment time was 5 days. Treatment cost could be <$10 year-1 (dairy cow)-1. Water dilution (3-fold) did not diminish the effectiveness of the carbonate/alkali treatment, and viability was <10 cells/g.
Research about dose-time-effect relation between rhubarb induced mouse diarrhoea tolerance and intestinal tract anthraquinone dynamic change. (2010)

Objective:Research the quantity-time-effect relation of Rhubarb induced mouse diarrhoea tolerance and intestinal tract anthraquinone dynamic change for reasonable useing Rhubarb in clinic.Methods:Low dose of Rhubarb was decided by its potency of decanta ED 95 ,high dose of Rhubarb was decided by two times of ED 95 .Mice are divided into blank group,every day low-dose group,every day high-dose group,every other day low-dose group,every other day high-dose group.Intragastric administrated every day and every other day 10 times.Water ratio,stool number,efflux time of Carbo Medicinalis are observed,and high performance liquid chromatogram(HPLC)are used to detect the ratio of yoked anthraquinone and liberated anthraquinone.Results:At same dose,Rhubarb Intragastric administrated every other day induced mouse costive more slight than other groups,after 10 times intragastric administration,every other day high-dose group's ratio of yoked anthraquinone and liberated anthraquinone was lower than every day high-dose group's.Conclusion:Interrupted administration may decrease Rhubarb induced diarrhoea tolerance.
ChemInform Abstract: NEUE SYNTH. FUER BICYCLO(2,2,2)OCTAN‐2,5‐DION (1973)

Abstract Isophoron (I) liefert mit Isopropenylacetat (II) die isomeren Enolester (III) bis (V), von denen die beiden ersteren nach Diels‐Alder mit 1‐Chlor‐1‐cyano‐ äthylen (VI) die Diels‐Alder‐Addukte (VII) und (VIII) liefern.
Computational Design of Metal Ion Sequestering Agents (2005)

Organic ligands that exhibit a high degree of metal ion recognition are essential precursors for developing separation processes and sensors for metal ions. Since the beginning of the nuclear era, much research has focused on discovering ligands that target specific radionuclides. Members of the Group 1A and 2A cations (e.g., Cs, Sr, Ra) and the f-block metals (actinides and lanthanides) are of primary concern to DOE. Although there has been some success in identifying ligand architectures that exhibit a degree of metal ion recognition, the ability to control binding affinity and selectivity remains a significant challenge. The traditional approach for discovering such ligands has involved lengthy programs of organic synthesis and testing that, in the absence of reliable methods for screening compounds before synthesis, have resulted in much wasted research effort. This project seeks to enhance and strengthen the traditional approach through computer-aided design of new and improved host molecules. Accurate electronic structure calculations are coupled with experimental data to provide fundamental information about ligand structure and the nature of metal-donor group interactions (design criteria). This fundamental information then is used in a molecular mechanics model (MM) that helps us rapidly screen proposed ligand architectures and select the best members from a set of potential candidates. By using combinatorial methods, molecule building software has been developed that generates large numbers of candidate architectures for a given set of donor groups. The specific goals of this project are: • further understand the structural and energetic aspects of individual donor group- metal ion interactions and incorporate this information within the MM framework • further develop and evaluate approaches for correlating ligand structure with reactivity toward metal ions, in other words, screening capability • use molecule structure building software to generate large numbers of candidate ligand architectures for given sets of donor groups • screen candidates and identify ligand architectures that will exhibit enhanced metal ion recognition. These new capabilities are being applied to ligand systems identified under other DOEsponsored projects where studies have suggested that modifying existing architectures will lead to dramatic enhancements in metal ion binding affinity and selectivity. With this in mind, we are collaborating with Professors R. T. Paine (University of New Mexico), K. N. Raymond (University of California, Berkeley), and J. E. Hutchison (University of Oregon), and Dr. B. A. Moyer (Oak Ridge National Laboratory) to obtain experimental validation of the predicted new ligand structures. Successful completion of this study will yield molecular-level insight into the role that ligand architecture plays in controlling metal ion complexation and will provide a computational approach to ligand design.
Identification and Structural Elucidation of Ergotryptamine, a New Ergot Alkaloid Produced by Genetically Modified Aspergillus nidulans and Natural Isolates of Epichloë Species (2014)

Ergot alkaloid pathway reconstruction in Aspergillus nidulans is an approach used to better understand the biosynthesis of these mycotoxins. An engineered strain named A. nidulans WFC (expressing ergot alkaloid synthesis genes dmaW, easF, and easC) produced the established intermediate N-methyl-4-dimethylallyltryptophan, as well as an uncharacterized ergot alkaloid. We investigated the chemical structure of the new metabolite and its role in the ergot alkaloid pathway. Mass spectrometry, labeling, and NMR studies showed that the unknown ergot alkaloid, designated here as ergotryptamine, differed from N-methyl-4-dimethylallyltryptophan by the loss of the carboxyl group, addition of a hydroxyl group, and shift in position of a carbon–carbon double bond. Feeding studies with Aspergillus mutants did not show ergotryptamine turnover, suggesting it is a pathway byproduct as opposed to an authentic intermediate. Several Epichloë species also produced this metabolite, and further investigations revealed the equivalency of ergotryptamine with an Epichloë-derived ergot alkaloid provisionally described as 6,7-secolysergine.
Raman Thermometry: Comparing Methods to Minimize Error. (2011)

Abstract not provided.
Ischemia-induced vascular changes: role of xanthine oxidase and hydroxyl radicals (1983)

The results of previous studies indicate that oxygen-derived free radicals are responsible for the increased vascular permeability produced by 1 h of intestinal ischemia. The aims of this study were 1) to test the hypothesis that the enzyme xanthine oxidase is the source of oxygen radicals in the ischemic bowel and 2) to assess the role of the hydroxyl radical in the ischemia-induced vascular injury. The capillary osmotic reflection coefficient was estimated from lymphatic protein flux data in the cat ileum for the following conditions: ischemia, ischemia plus pretreatment with allopurinol (a xanthine oxidase inhibitor), and ischemia plus pretreatment with dimethyl sulfoxide (a hydroxyl radical scavenger). The increased vascular permeability produced by ischemia was largely prevented by pretreatment with either allopurinol or dimethyl sulfoxide. These findings support the hypothesis that xanthine oxidase is the source of oxygen radicals produced during ischemia. The results also indicate that hydroxyl radicals, derived from the superoxide anion, are primarily responsible for the vascular injury associated with intestinal ischemia.
Tumour necrosis factor‐α receptor 1 polymorphisms and serum soluble TNFR1 in early spontaneous miscarriage (2007)

The data do not provide evidence that TNFR1 gene polymorphism is etiologically important for ERSM in Chinese women. But, a significantly raised sTNFR1 level in non-pregnant ERSM women was recorded compared to women with normal pregnancies. The result suggests that pregnancy failure is associated with an increase of sTNFR1.
Changes in E2F binding after phenylbutyrate-induced differentiation of Caco-2 colon cancer cells. (2000)

Differentiation agents use existing cellular systems to induce neoplastic cells to regain a normal phenotype and/or to cause growth arrest and therefore may offer novel chemotherapeutic approaches to treating solid tumors. In this study, we demonstrate in Caco-2 colon cancer cells that the differentiation agent phenylbutyrate (PB) causes a decrease in viable cells, an increase in cell differentiation, and a G1-S-phase block. The mechanism of this last effect is related to a PB-induced increase in p27Kip1, leading to a decrease in the activity of cyclin-dependent kinase 2 (CDK2), a positive regulator of the G1-S-phase cell cycle transition. Consistent with the decreased CDK2 kinase activity, we also observed a decrease in the phosphorylation state of the retinoblastoma protein after PB treatment. This was associated with increased binding and consequent inactivation of E2F, a transactivator of genes that regulate the G1 to S phase cell cycle transition. These data suggest that the differentiation agent PB inhibits tumor growth by limiting the availability of active E2F, with a subsequent G1-S-phase block. Additional studies should show whether PB is a clinically effective therapeutic agent against colorectal cancer.
A low-resource public-key identification scheme for RFID tags and sensor nodes (2009)

We revisit a public key scheme presented by Shamir in [19] (and simultaneously by Naccache in [15]) and examine its applicability for general-purpose RFID tags in the supply chain. Using a combination of new and established space-saving methods, we present a full-fledged public key identification scheme, which is secure yet highly efficient. The 1024-bit scheme fits completely (including RAM) into 4682 gate equivalents and has a mean current consumption of 14.2μA. The main novelty in our implementation is the replacement of the long pseudo-random sequence, originally stored on 260 bytes of EEPROM in [19], by a reversible stream cipher using less than 300 bits of RAM. We show how our scheme offers tag-to-reader and reader-to-tag authentication and how it can be fit into the existing RFID supply chain infrastructure.
A novel free radical scavenger, NSP-116, ameliorated the brain injury in both ischemic and hemorrhagic stroke models (2019)

Reperfusion injury is a serious problem in ischemic stroke therapy, which leads to neuronal damage and intracranial hemorrhage (ICH). A novel free radical scavenger, NSP-116, has anti-oxidative effect and may ameliorate reperfusion injury. The purpose of this study was to investigate the effects of NSP-116 on both ischemic and hemorrhagic stroke models. First, we assessed whether NSP-116 has protective effects in vitro. Pre-treatment of NSP-116 decreased neuronal cell damage induced by H<sub>2</sub>O<sub>2</sub> or LPS. Moreover, NSP-116 also suppressed mitochondria damage and apoptosis in H<sub>2</sub>O<sub>2</sub>-induced neuronal injury model. Based on these results, we used a middle cerebral artery occlusion (MCAO)-induced ischemic stroke model or a collagenase-induced ICH model. Using the MCAO model, we evaluated the cerebral blood flow (CBF), neurological deficit, and infarct volume. Hematoma volume was assessed at 3 days after ICH. In the MCAO model, oral administration of NSP-116 at 30 mg/kg attenuated the reduction of CBF, neurological deficits, and infarct formation. Interestingly, NSP-116 also ameliorated hematoma expansion and neurological deficits in the ICH model. Additionally, pre-treatment of NSP-116 suppressed the brain microvascular endothelial cell death induced by collagenase treatment. Collectively, our findings indicated that oral administration of NSP-116 attenuates both ischemic and hemorrhagic brain injuries after stroke.
High-Throughput Screening of Nitrogen-Coordinated Bimetal Catalysts for Multielectron Reduction of CO₂ to CH₄ with High Selectivity and Low Limiting Potential (2021)

Significant challenges remain for developing efficient catalysts in an electrochemical multielectron CO2 reduction reaction (CO2RR), which usually suffers from poor activity and selectivity. Motivated by the recent experimental progress in fabricating dual-metal atom catalysts (DMACs) in N-doped graphene materials (graphene-N6V4; N: nitrogen and V: vacancy), we sampled eight types of homonuclear (N6V4-M-2, M = Cr, Mn, Fe, Co, Ni, Cu, Pd, and Ag) catalysts and 28 types of heteronuclear (N6V4-M1M2) catalysts to study CO2RR activity via first-principles high-throughput screening. Using stability, activity, and selectivity as indicators along with the broken conventional scaling relationship, N6V4-AgCr was selected as a promising candidate for deep CO2 reduction to methane with a low overpotential of 0.55 V after two screening rounds. Further analysis showed that a frustrated Lewis pair, formed between metal and the para-N, owing to the difference in the electronic arrangement of the d orbitals of various transition metals, caused a difference in the spin polarization of the systems and affected the catalytic performance of each DMAC. Our work not only provides a solid strategy for screening potential catalysts but also demonstrates that their CO2 reduction activities originate from the various atomic and electronic structures of DMACs.
A novel spectrofluorimetric method based on a reaction with an azoisoxazoles–benzenesulfonamide derivative for determination of uranium (VI) ions in water samples (2022)

Selective fluorometric detection and determination of uranium ions is provided here using a novel fluorescent reagent, namely (E)-4-([4-hydroxynaphthalen-1-yl]diazenyl)-N-(5-methyleisoxazol-3-yl) benzenesulfonamide (U<sup>VI</sup> reagent). The U<sup>VI</sup> reagent offers a selective fluorescence enhancement behaviour at emission wavelength = 557 nm. The parameters affecting fluorometric detection of uranium ions, such as the pH, solvent type, ligand concentration, interaction time, and interfering ions, were investigated and adjusted. The proposed U<sup>VI</sup> reagent can detect and determine uranium ions even at low concentrations, for which the obtained limit of detection was 0.1 ppm. Additionally, this proposed determination protocol was successfully used to detect, monitor, and determine uranium ions in actual water samples.
Fabrication of Magnetic Tunnel Junctions with a Single-Crystalline LiF Tunnel Barrier (2017)

We fabricated Fe/LiF/Fe magnetic tunnel junctions (MTJs) by molecular beam epitaxy on a MgO(001) substrate, where LiF is an insulating tunnel barrier with the same crystal structure as MgO (rock-salt type). Crystallographical studies such as transmission electron microscopy and nanobeam electron diffraction observations revealed that the LiF tunnel barrier is single-crystalline and has a LiF(001)[100] ∥ bottom Fe(001)[110] crystal orientation, which is constructed in the same manner as MgO(001) on Fe(001). Also, the in-plane lattice mismatch between the LiF tunnel barrier and the Fe bottom electrode was estimated to be small (about 0.5%). Despite such advantages for the tunnel barrier of the MTJ, the observed tunnel magnetoresistance (MR) ratio was low (~6% at 20 K) and showed a significant decrease with increasing temperature (~1% at room temperature). The results imply that indirect tunneling and/or thermally excited carriers in the LiF tunnel barrier, in which the current basically is not spin-polarized, play a major role in electrical transport in the MTJ.
Catalytic Enantioselective Synthesis of Glutamic Acid Derivatives via Tandem Conjugate Addition—Elimination of Activated Allylic Acetates under Chiral PTC Conditions. (2006)

A new, general, and practical procedure for the asymmetric synthesis of 4-alkylidenyl glutamic acid derivatives via a catalytic enantioselective tandem conjugate addition−elimination on allylic acetates under chiral phase-transfer conditions is reported. A variety of structural types of allylic acetates have been reacted with the benzophenone imine of glycine &lt;i&gt;tert&lt;/i&gt;-butyl ester to give the products in good to excellent yields and enantioselectivities (63−92% yield, 80−97% ee, 8 cases).
IR absorption spectra for PCE, TCE, DCE, and VC molecules using density functional theory (2019)

Calculations are presented of vibrational absorption spectra for PCE, TCE, DCE and VC molecules using density function theory (DFT). These ground water contaminants are among the most widely spread carcinogens in the environment of industrial countries. DFT calculated absorption spectra of isolated molecules represent quantitative estimates that can be correlated with additional information obtained from laboratory measurements. The chlorohydrocarbons, whose spectra are calculated, are characterized by an interconnected equilibrium network. The simultaneous knowledge of the spectrum of each molecule within this network will be useful for detection and monitoring of the water contaminants. The DFT software GAUSSIAN was used for the calculations of the infrared (IR) spectra presented here.
Direct structural evidence of commensurate-to-incommensurate transition of hydrocarbon adsorption in a microporous metal organic framework (2015)

The efficiency of physisorption-based separation of gas-mixtures depends on the selectivity of adsorbent which is directly linked to size, shape, polarizability and other physical properties of adsorbed molecules. Commensurate adsorption is an interesting and important adsorption phenomenon, where the adsorbed amount, location, and orientation of an adsorbate are commensurate with the crystal symmetry of the adsorbent. Understanding this phenomenon is important and beneficial as it can provide vital information about adsorbate-adsorbent interaction and adsorption-desorption mechanism. So far, only sporadic examples of commensurate adsorption have been reported in porous materials such as zeolites and metal organic frameworks (MOFs). In this work we show for the first time direct structural evidence of commensurate-to-incommensurate transition of linear hydrocarbon molecules (C<sub>2</sub>-C<sub>7</sub>) in a microporous MOF, by employing a number of analytical techniques including single crystal X-ray diffraction (SCXRD), <i>in situ</i> powder X-ray diffraction coupled with differential scanning calorimetry (PXRD-DSC), gas adsorption and molecular simulations.
Plasminogen activator inhibitor type 2 is expressed in keratinocytes during re-epithelialization of epidermal defects (1998)

Plasminogen activation is observed in the human epidermis during re-epithelialization of epidermal defects. The activation reaction depends on plasminogen activators (PAs) associated with re-epithelializing keratinocytes. PA inhibitor type 2 (PAI-2) is thought to be a major epidermal PA inhibitor in keratinocytes. However, no data are available on the expression of PAI-2 in keratinocytes during epidermal regeneration. We have therefore analysed PAI-2 at the mRNA and protein level in keratinocyte cultures as well as in epidermal lesions in which re-epithelializing keratinocytes were apparent. We found that PAI-2 expression at the mRNA and protein level was negatively correlated with the cell density in regular keratinocyte cultures. In organotypic cocultures, in which the transition from a re-epithelializing to a sedentary phenotype can be studied, PAI-2 was most strongly expressed in early cultures prior to formation of a differentiated epidermis-like structure. We found a strong expression of PAI-2 in keratinocytes that re-epithelialized dermal burn wounds or lesions caused by the autoimmune blistering disease pemphigus vulgaris. Our results suggest that not only PAs, but also a major PA inhibitor, PAI-2, are expressed in keratinocytes that are actively involved in re-epithelialization.
[Progress in the research of caffeine metabolism and its application in vivo]. (2010)

Caffeine, a kind of alkaloid, extracted from tea and coffee fruit, is commonly used in the treatment of neurasthenia and for coma recovery. The metabolic process of caffeine in vivo is complex. Fifteen kinds of metabolites have been found, and the enzymes involved in the metabolic processes have also been confirmed. The urinary caffeine metabolites ratios are commonly used in the assessment of activities of drug metabolizing enzymes, mainly including CYP1A2, CYP2A6, N-acetyltransferase and xanthine oxidase. Methods for detection of caffeine and its metabolites have been improved steeply. In brief, caffeine has been paid close attention due to its intimate connection with human health as well as its importance in application in scientific research.