gebhart/patrepeval huggingface dataset:
Three distinct 3-methylcytidine (m3C) methyltransferases modify tRNA and mRNA in mice and humans (2017)

Chemical RNA modifications are central features of epitranscriptomics, highlighted by the discovery of modified ribonucleosides in mRNA and exemplified by the critical roles of RNA modifications in normal physiology and disease. Despite a resurgent interest in these modifications, the biochemistry of 3-methylcytidine (m<sup>3</sup>C) formation in mammalian RNAs is still poorly understood. However, the recent discovery of <i>trm141</i> as the second gene responsible for m<sup>3</sup>C presence in RNA in fission yeast raises the possibility that multiple enzymes are involved in m<sup>3</sup>C formation in mammals as well. Here, we report the discovery and characterization of three distinct m<sup>3</sup>C-contributing enzymes in mice and humans. We found that methyltransferase-like (METTL) 2 and 6 contribute m<sup>3</sup>C in specific tRNAs and that METTL8 only contributes m<sup>3</sup>C to mRNA. MS analysis revealed that there is an ∼30-40% and ∼10-15% reduction, respectively, in <i>METTL2</i> and <i>-6</i> null-mutant cells, of m<sup>3</sup>C in total tRNA, and primer extension analysis located METTL2-modified m<sup>3</sup>C at position 32 of tRNA<sup>Thr</sup> isoacceptors and tRNA<sup>Arg(CCU)</sup> We also noted that METTL6 interacts with seryl-tRNA synthetase in an RNA-dependent manner, suggesting a role for METTL6 in modifying serine tRNA isoacceptors. <i>METTL8</i>, however, modified only mRNA, as determined by biochemical and genetic analyses in <i>Mettl8</i> null-mutant mice and two human <i>METTL8</i> mutant cell lines. Our findings provide the first evidence of the existence of m<sup>3</sup>C modification in mRNA, and the discovery of METTL8 as an mRNA m<sup>3</sup>C writer enzyme opens the door to future studies of other m<sup>3</sup>C epitranscriptomic reader and eraser functions.
Determination of Forage Quality by near Infrared Reflectance Spectroscopy: Efficacy of Broad-Based Calibration Equations (1987)

Two experiments were conducted to determine 1) if statistical clustering of near infrared spectra would aid in selection of samples to establish calibration equations, and 2) if broad-based calibration equations were capable of accurately determining forage quality. In Experiment !, clustering of spectra did not have any advantage over random selection as a means to select samples. In Experiment 2, 990 hay samples representing a large diversity of species, maturity, cutting, and chemical composition, were collected from 3i states. Approximately 50% of the samples were used in this study. Samples were separate d into calibration and Validation sets, either on a random basis or by subset of samples from individual states into validation sets. Based on randomly selected Samples, the
Photochemical Coenzyme Regeneration in an Enzymatically Active Optical Material (2004)

The photoinduced electron transfer between immobilized thionine and the dinucleotide enzyme cofactors NADH and NADPH in a SiO2 sol−gel matrix is reported. The electron-transfer quenching of thionine luminescence is used to monitor the rate of NADPH oxidation. Using Stern−Volmer quenching curves, the quenching rates in the silica matrix are 1 to 2 orders of magnitude smaller than those in solution. The rate constants for oxidation of NADPH by thionine were measured to be 9.8(±2.9) × 10-3 s-1 in solution and 8.8(±1.0) × 10-4 s-1 in the gel. Within the silica matrix, the photoinduced oxidation of NADPH is combined with the enzymatic reaction of isocitrate dehydrogenase, which uses the oxidized cofactor, NADP+, as an electron acceptor in the oxidation of isocitrate. The encapsulated isocitrate dehydrogenase is active with a Michaelis−Menten constant, KM, of 3 μM and a kcat of 0.67 μM/s per mgenzyme. Because optical sensors use NADPH fluorescence as an indicator of the presence and relative concentration of enzyme substrate, the successful demonstration of photoinduced regeneration of NADP+ makes possible continuous monitoring by the family of dehydrogenase enzymes.
Statistical methods in computational anatomy (1997)

This paper reviews recent developments by the Washington/Brown groups for the study of anatomical shape in the emerging new discipline of computational anatomy. Parametric representations of anatomical variation for computational anatomy are reviewed, restricted to the assumption of small deformations. The generation of covariance operators for probabilistic measures of anatomical variation on coordinatized submanifolds is formulated as an empirical procedure. Populations of brains are mapped to common coordinate systems, from which template coordinate systems are constructed which are closest to the population of anatomies in a minimum distance sense. Variation of several one-, two- and three-dimensional manifolds, i.e. sulci, surfaces and brain volumes are examined via Gaussian measures with mean and covariances estimated directly from maps of templates to targets. Methods are presented for estimating the covariances of vector fields from a family of empirically generated maps, posed as generalized spectrum estimation indexed over the submanifolds. Covariance estimation is made parametric, analogous to autoregressive modelling, by introducing small deformation linear operators for constraining the spectrum of the fields.
Detection of the extracellular proteases of Bacteroides nodosus in polyacrylamide gels: a rapid method of distinguishing virulent and benign ovine isolates. (1983)

The extracellular proteases of Bacteroides nodosus were separated electrophoretically on polyacrylamide slab gels at pH 8 . 8. Proteolytic activity was detected by placing the gel slab on a layer of gelatin-agar and allowing hydrolysis of the gelatin to occur. After two hours at 37 degrees C, the unhydrolysed gelatin was precipitated with mercuric chloride in acid. The proteolytic zymograms of 14 benign strains were identical. The zymograms of 10 virulent strains yielded two closely related sets of proteases. The reproducible difference observed between the respective zymograms readily provides a rapid diagnostic test to assist in the identification of benign and virulent strains of B nodosus.
Tetracyclines tigecycline and doxycycline inhibit LPS-induced nitric oxide production by RAW 264.7 murine macrophages. (101.3) (2007)

Abstract We previously reported that minocycline and doxycycline strongly suppress serum IgE and decrease IgE production by PBMC from patients with asthma (Smith-Norowitz et al, Ann Allergy, Asthma, &amp; Immunol 2002; 89:172–9; Durkin et al, AAAAI Annual Meeting San Diego, Feb 23–27, 2007). We have now studied the effects of doxycycline and tigecycline on LPS-induced nitric oxide (NO) production by murine macrophages (RAW 264.7). Cell cultures were incubated for 1 – 5 days with or without LPS (200ng/mL, phenol extracted from Salmonella typhimurium) and doxycycline or tigecycline (1 – 10 μg/ml). Accumulation of nitrite, stable metabolite of NO, was determined using a modified colorimetric Griess reaction. Both doxycycline, and to a lesser extent tigecycline, consistently suppressed LPS-induced nitric oxide production in dose-dependent manner (doxycycline: 23–30%, tigecycline: 10–23%). The tetracycline mediated suppression of NO production by macrophages in culture is independent of antimicrobial activities, but the underlying mechanism of this effect remains to be elucidated. Since nitric oxide is an important mediator of inflammatory responses, our results suggest that the anti-inflammatory effects of tetracyclines may be utilized in the treatment of IgE mediated allergic disorders and may decrease exhaled breath nitric oxide, an emerging biomarker of allergic airway disease.
Differential ratings of pleasantness following right and left hemispheric application of low energy magnetic fields that stimulate long-term potentiation (1994)

A total of 40 normal men and women were exposed under double blind conditions for 20 min to either sham-conditions or to 1 microT (10 mG) electromagnetic fields (known to produce long-term potentiation within hippocampal slices) that were applied primarily over the right temporal lobe, over the left temporal lobe or over both temporal lobes homogeneously. The men and women who received the stimulation over the right hemisphere rated their experiences as significantly more pleasant than those who received the same stimulation over the left hemisphere [eta = 0.51]. Covariance for the variation in ambient geomagnetic activity, which was negatively correlated with pleasantness, increased the significance of the experimental treatment. The potential clinical utility of applying computer-generated local and penetrative but weak intensity complex magnetic fields over portions of the human brain is discussed.
Genetic transformation of clone rootstock of stone fruits 146-2 using the green fluorescent protein reporter gene (2022)

For the form of dwarf winter-hardy clonal rootstocks of stone crops 1 46-2 ( Prunus pumila L.x P.tomentosa Thunb . ), system of regeneration and genetic transformation using green fluorescent protein (GFP) has been developed. For eff ective regeneration of accessory shoots, no pre-treatment with 6-benzylamine-purine (BA) and auxin was required. Stimulation of the regeneration of shoots from leaf explants required 2-3 weeks of a dark period. Th e best percentage of regeneration (greater than 75 %) was observed with a combination of 3 mg/L BA and 0.75 mg/L IBA. The achieved regeneration effi ciency made it possible to develop a protocol for genetic transformation, mediated by Agrobacterium , for rootstock 146-2. Whole leaves from in vitro-cultured shoots were used as explants for transformation by the A. tumefaciens strain CBE21, with the binary vector pBINmGFP5ER containing the nptII encoding neomycin phosphotransferase II as a plant-selectable marker under the control of the NOS promoter (nopalin synthase) and the reporter gfp gene encoding a green fluorescent protein under the control of the cauliflower mosaic virus (CaMV) promoter 35S. Th e integration of nptII and gfp into transgenes was confirmed by PCR. Expression of the green fluorescent protein was observed using fluorescence microscopy. The efficiency of transformation based on PCR analysis of independent lines resistant to kanamycin was 0.41-0.83 %. All transgenic lines showed resistance to kanamycin at a concentration of 40 mg/L. They were rooted and acclimatized to greenhouse conditions. Th e developed protocols will be used to produce Plum pox virus (PPV) resistant plants.
The molecular and neural regulation of ultraviolet light phototaxis and its food-associated learning behavioral plasticity in C. elegans (2021)

Ultraviolet light is quite toxic to all the animals and evoke the avoidance behavior of UV. The soil nematode Caenorhabditis elegans senses UV and is known to avoid UV by using four sensory neurons. However, it is not clear what signaling molecules act for UV avoidance in the neuronal pathway constituted of four sensory neurons. In addition, it is not clear whether this harmful environmental signal can be associated with other benefit signals such as food. In this study, by using newly developed assay system, we found that C. elegans can associate UV and food and changes behavioral strategy against harmful UV signal. This is the first indication that C. elegans shows associate learning with UV and food. Using our assay system, we also found that glutamate is used as a transmitter in both the UV avoidance and UV associate learning neural circuits. However, one sensory neuron showed a significant role for associative learning, compared to a complimentary role in four sensory neurons for direct associative learning, and different sets of glutamate receptors seemed to be acting for UV avoidance and UV associate learning. These findings suggest that a distinct neuronal network is used for UV learning compared to that for direct avoidance behavior of UV.
Plant recombinant erythropoietin attenuates inflammatory kidney cell injury (2008)

Human erythropoietin (EPO) is a pleiotropic cytokine with remarkable tissue-protective activities in addition to its well-established role in red blood cell production. Unfortunately, conventional mammalian cell cultures are unlikely to meet the anticipated market demands for recombinant EPO because of limited capacity and high production costs. Plant expression systems may address these limitations to enable practical, cost-effective delivery of EPO in tissue injury prevention therapeutics. In this study, we produced human EPO in tobacco and demonstrated that plant-derived EPO had tissue-protective activity. Our results indicated that targeting to the endoplasmic reticulum (ER) provided the highest accumulation levels of EPO, with a yield approaching 0.05% of total soluble protein in tobacco leaves. The codon optimization of the human EPO gene for plant expression had no clear advantage; furthermore, the human EPO signal peptide performed better than a tobacco signal peptide. In addition, we found that glycosylation was essential for the stability of plant recombinant EPO, whereas the presence of an elastin-like polypeptide fusion had a limited positive impact on the level of EPO accumulation. Confocal microscopy showed that apoplast and ER-targeted EPO were correctly localized, and N-glycan analysis demonstrated that complex plant glycans existed on apoplast-targeted EPO, but not on ER-targeted EPO. Importantly, plant-derived EPO had enhanced receptor-binding affinity and was able to protect kidney epithelial cells from cytokine-induced death in vitro. These findings demonstrate that tobacco plants may be an attractive alternative for the production of large amounts of biologically active EPO.
On the base catalysed ring opening of 3-unsubstituted isoxazoles. Derivatives of 4- and 5-phenylisoxazole (1977)

The kinetics of the base-induced decomposition of 4- and 5-phenylisoxazole and their p-bromo- and p-nitrophenyl derivatives, and 3-deuterio-5-phenylisoxazole, to the corresponding cyanoenolate anions have been studied. The mechanism of reaction has been established as a one-stage concerted abstraction of the proton in position 3 and scission of the N–O bond. 4-Phenylisoxazole, previously synthesized by laborious methods, has been prepared by a simpler procedure.
Interhelical Interactions in the gp41 Core:  Implications for Activation of HIV-1 Membrane Fusion, (2002)

The human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein complex (gp120-gp41) promotes viral entry by mediating the fusion of viral and cellular membranes. Formation of a stable trimer-of-hairpins structure in the gp41 ectodomain brings the two membranes into proximity, leading to membrane fusion. The core of this hairpin structure is a six-helix bundle in which three carboxyl-terminal outer helices pack against an inner trimeric coiled coil. Here we investigate the role of these conserved interhelical interactions on the structure and function of both the envelope glycoprotein and the gp41 core. We have replaced each of the eight amino acids at the buried face of the carboxyl-terminal helix with a representative amino acid, alanine. Structural and physicochemical characterization of the alanine mutants shows that hydrophobic interactions are a dominant factor in the stabilization of the six-helix bundle. Alanine substitutions at the Trp628, Trp631, Ile635, and Ile642 residues also affected envelope processing and/or gp120-gp41 association and abrogated the ability of the envelope glycoprotein to mediate cell-cell fusion. These results suggest that the amino-terminal region of the gp41 outer-layer alpha-helix plays a key role in the sequence of events associated with HIV-1 entry and have implications for the development of antibodies and small-molecule inhibitors of this conserved element.
A New Method to Enhance the Accuracy of the Buckling Test Using Modified Yoshida Sample (2014)

Because of the extensive use of thin sheet metals to reduce the weight of vehicles, wrinkling is becoming a more common and one of the most undesirable failures in the sheet forming process. Generally, experiments for studying wrinkling phenomena can be divided into two methods: actual forming of typical parts such as annular cup test on the one hand and the tests of specially designed sample geometries like the Yoshida Buckling test on the other. Recent experiments indicate that the plastic strains at the onset of wrinkling in the Buckling Test with Yoshida samples are too small to reflect reality of deep and stretch drawing conditions. Therefore, in this paper, in order to enhance the accuracy of the prediction of wrinkling, a new modified Yoshida specimen is provided for numerical simulation. The fundaments of the different buckling phenomena are going to be explained considering the energy theory in metal forming processes. Meanwhile, the influences of the changeable sample geometries in order to cause different stress distribution within loaded area of specimen have been investigated.
Inhibition of matrix metalloproteinase-9 by “multi-prong” surface binding groups (2005)

A novel strategy of blocking the active site accessibility of MMP-9 by "multi-prong" surface binding groups is described.
Read-out electronics for digital silicon photomultiplier modules (2013)

This work has its focus on the development of fast read-out electronics for digital silicon photomultipliers (dSiPM -called Digital Photon Counter (DPC) by Philips).
Bulk copolymerization of styrene‐acrylic esters: Some analysis and design considerations (1983)

Abstract A common framework for the analysis of styrene‐acrylic ester systems has been developed by analyzing the pertinent kinetic information. This is shown to lead to a well defined strategy for the design of copolymerization reactors especially in the industrially relevant high conversion region. The existence of stable steady states and its influence on the system parameters has been illustrated for the case of a continuous stirred tank reactor (CSTR). A novel strategy of a CSTR operated with a recycle is proposed. This is shown to lead to an operation in the unique steady state with the added advantage of a high conversion and uniform copolymer composition. This would seem to be the first such analysis in the high conversion region.
Enterprise architecture: definition, content, and utility (2002)

Although the concept of an enterprise architecture (EA) has not been well defined and agreed upon, EAs are being developed to support information system development and enterprise reengineering. Most EAs differ in content and nature, and most are incomplete because they represent only data and process aspects of the enterprise. This paper defines an EA. Basic EA concepts are presented. The purpose and utility of an EA and its place in the information system environment are discussed. To facilitate understanding, a generic EA is provided. Through the generic model, each major component of an EA is defined and the component's purpose and use are presented. The generic EA described here will be used to develop enterprise-specific EAs. This paper emphasizes linkages between the EA and information systems development by depicting the information systems viewpoint. To delineate how an EA is useful in the information technology (IT) world, this paper shows how an EA relates to both an information systems architecture (ISA) and an information architecture (IA).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Surfactant Effect On Foam: From Core Flood Experiments To Implicit-Texture Foam-Model Parameters (2016)

Abstract Aqueous foams play an important role in many industrial processes, from ore separation by froth flotation to enhanced oil recovery (EOR), where the foam is used as a means of increasing sweep efficiency through oil-bearing rock. The complex, structure-dependent, flow behavior of the foam gives improved penetration of lower-permeability regions. Foam is stabilized by surfactant molecules, and the foam strength is influenced by the surfactant concentration in the water phase. It is therefore of great importance to understand the effect of surfactant concentration on foam processes. Implicit Texture (IT) foam models eg STARS account for the surfactant effect with functions that depend on surfactant concentration in the water and a few other parameters. However, there is no evidence that these functions are able to capture adequately the effect of surfactant concentration effect. We present a comparative study of foam core-flood experiments with various surfactant concentrations. Core-flood tests were conducted in rock cores with a diameter of 1 cm and length of 17cm, significantly smaller than typical cores. Plots of apparent viscosity vs. injected gas fraction were obtained for surfactant concentrations at the critical micellar concentration (CMC) and above. Bulk foam stability and surface tension were measured for all concentrations, in order to define the CMC and to compare with coreflood results. The experimental results have been matched with the STARS IT foam model and the dependency of model parameters on the surfactant concentration is discussed. This work found that the IT model is not able to predict the decrease of the foam strength with decreasing surfactant concentration. Instead, the study shows that the effect of surfactant concentration can be correlated with the dry-out function of the IT model, and specifically to the limiting capillary pressure
A Review of the Efficacy of Silicon Carbide Hot-Gas Filters in Coal Gasification and Pressurized Fluidized Bed Combustion Environments (1996)

Reviews of relevant literature and interviews with individuals cognizant of the state of the art in ceramic filters for hot-gas cleaning were conducted. Thermodynamic calculations of the stability of various ceramic phases were also made. Based on these calculations, reviews, and interviews, conclusions were reached regarding the use of silicon carbide-based ceramics as hot-gas filter media. Arguments are presented that provide the basis for our conclusion that high-purity silicon carbide is a viable material in the integrated coal gasification combined cycle (IGCC) and pressurized fluidized-bed combustion (PFBC) environments we examined. Clay-bonded materials are, we concluded, suspect for these applications, their extensive use not-withstanding. Operations data we reviewed focused primarily on clay-bonded filters, for which a great deal of experience exists. We used the clay-bonded filter experience as a point of reference for our review and analysis.
Current Best Practices for Respiratory Virus Testing (2011)

ABSTRACT Diagnostic testing for respiratory viruses has been revolutionized by recent advances that have made rapid and highly accurate tests accessible to clinical laboratories, and it is important that these improved methods be utilized. Accurate detection of respiratory viruses is important in patient care, as it guides both therapy and infection control measures. On a larger scale, the CDC and its collaborating laboratories collect both data and isolates from clinical laboratories for national surveillance, and the use of high-quality tests in clinical laboratories can improve the quality of these data.
New perspectives on forbidden symmetries, quasicrystals, and Penrose tilings (1996)

Quasicrystals are solids with quasiperiodic atomic structures and symmetries forbidden to ordinary periodic crystals-e.g., 5-fold symmetry axes. A powerful model for understanding their structure and properties has been the two-dimensional Penrose tiling. Recently discovered properties of Penrose tilings suggest a simple picture of the structure of quasicrystals and shed new light on why they form. The results show that quasicrystals can be constructed from a single repeating cluster of atoms and that the rigid matching rules of Penrose tilings can be replaced by more physically plausible cluster energetics. The new concepts make the conditions for forming quasicrystals appear to be closely related to the conditions for forming periodic crystals.