gebhart/patrepeval huggingface dataset:
Purification and properties of dinitrogenase reductase ADP-ribosyltransferase from the photosynthetic bacterium Rhodospirillum rubrum. (1988)

The enzyme that catalyzes the ADP-ribosylation and concomitant inactivation of dinitrogenase reductase in Rhodospirillum rubrum has been purified greater than 19,000-fold to near homogeneity. We propose dinitrogenase reductase ADP-ribosyltransferase (DRAT) as the working name for the enzyme. DRAT activity is stabilized by NaCl and ADP. The enzyme is a monomer with a molecular mass of 30 kDa and is a different polypeptide than dinitrogenase reductase activating glycohydrolase. NAD (Km = 2 mM), etheno-NAD, nicotinamide hypoxanthine dinucleotide, and nicotinamide guanine dinucleotide will serve as donor molecules in DRAT-catalyzed ADP-ribosylation reaction, and dinitrogenase reductases from R. rubrum, Azotobacter vinelandii, Klebsiella pneumoniae, and Clostridium pasteurianium will serve as acceptors. No other proteins or small molecules, including water, have been found to be effective as acceptors. Nicotinamide is released stoichiometrically with formation of the ADP-ribosylated product. DRAT is inhibited by NaCl and has maximal activity at a pH of 7.0.
11C-Labeling of Aryl Ketones as Candidate Histamine Subtype-3 Receptor PET Radioligands through Pd(0)-Mediated 11C-Carbonylative Coupling (2017)

Pd(0)-mediated coupling between iodoarenes, [<sup>11</sup>C]carbon monoxide and aryltributylstannanes has been used to prepare simple model [<sup>11</sup>C]aryl ketones. Here, we aimed to label four 2-aminoethylbenzofuran chemotype based molecules ([<sup>11</sup>C]<b>1</b>-<b>4</b>) in the carbonyl position, as prospective positron emission tomography (PET) radioligands for the histamine subtype 3 receptor (H3R) by adapting this methodology with use of aryltrimethylstannanes. Radiosynthesis was successfully performed on a platform equipped with a mini-autoclave and a liquid handling robotic arm, within a lead-shielded hot-cell. Candidate radioligands were readily formulated in saline containing ethanol (10%, <i>v</i>/<i>v</i>) and ascorbic acid (0.5 mg/10 mL). Yields for preclinical use were in the range of 5-9%, decay-corrected from cyclotron-produced [<sup>11</sup>C]CO₂ and molar activities were >115 GBq/µmol at end of synthesis. Radiochemical purities exceeded >97%.
X-ray diffraction study of the polymorphic behavior of N-methylated dioleoylphosphatidylethanolamine (1988)

The polymorphic phase behavior of aqueous dispersions of dioleoylphosphatidylethanolamine (DOPE) and its N-methylated analogues, DOPE-Me, DOPE-Me2, and DOPC, has been investigated by X-ray diffraction. In the fully hydrated lamellar (L alpha) phase at 2 degrees C, the major structural difference is a large increase in the interlamellar water width from DOPE to DOPE-Me, with minor increases with successive methylation. Consistent with earlier reports, inverted hexagonal (HII) phases are observed upon heating at 5-10 degrees C in DOPE and at 65-75 degrees C in DOPE-Me and are not observed to at least 85 degrees C in DOPE-Me2 or DOPC. In DOPE, the L alpha-HII transition is facile and is characterized by a relatively narrow temperature range of coexistence of L alpha and HII domains, each with long-range order. DOPE-Me exhibits complex nonequilibrium behavior below the occurrence of the HII phase: Upon heating, the L alpha lattice spontaneously disorders on a time scale of days; on cooling from the HII phase, the disorder rises on a time scale of minutes. It is shown that, in copious water, the disordered state transforms very slowly into phases with cubic symmetry. This process is assisted by the generation of small amounts of lipid degradation products. The relative magnitudes of the monolayer spontaneous radius of curvature, R0 [Kirk, G. L., Gruner, S. M., & Stein, D. L. (1984) Biochemistry 23, 1093; Gruner, S. M. (1985) Proc. Natl. Acad. Sci. U.S.A. 82, 3665], are inferred from the HII lattice spacings vs temperature and are shown to increase with increasing methylation. The relative magnitudes of R0 are categorized as small for DOPE, intermediate for DOPE-Me, and large for DOPC. It is suggested, and examples are used to illustrate, that small R0 lipid systems exhibit facile, low-temperature L alpha-HII transitions, intermediate R0 systems exhibit complex nonequilibrium transition behavior and are likely to form cubic phases, and large R0 systems are stable as L alpha phases. The relationship between the cubic phases and minimal periodic surfaces is discussed. It is suggested that minimal periodic surfaces represent geometries in which near constant, intermediate R0 values can be obtained concomitantly with monolayers of near constant thickness, thereby leading to equilibrium cubic phases. Thus, the relative magnitude of the spontaneous radius of curvature may be used to predict mesomorphic behavior.(ABSTRACT TRUNCATED AT 400 WORDS)
Cochlear modeling - 1980 (2005)

A general review of the present state of cochlear mechanical modeling is presented in this paper, and some new experimental neural phase data is discussed and compared to a recent theory of hair cell transduction. This theory of transduction unifies experimental mechanical and neural tuning data while it simultaneously predicts a 180° phase shift in the neural response one octave below CF. The new phase measurements qualitatively collaborate this transduction theory. The intent of this paper is to be somewhat philosophical about the future directions of cochlear modeling and cochlear theory and it attempts to provide an alternatively explanation of many widely accepted diverse experimental results.
PI-4 Trogocytosis of viral immune complexes in the context of HIV-1 infection (2019)

Fc-mediated Ab functions rely on multiple mechanisms of action that include the recruitment of complement and Fc receptor-bearing cellular subsets that can mediate trogocytosis, phagocytosis, and cellular cytotoxicity. Monocytes-mediated trogocytosis is defined as the active exchange of membrane fragments between cells tightly interacting through an immunological synapse. Here, we propose to define the trogocytic activity of anti-Envelope human monoclonal antibodies in the context of HIV-1 infection. With this aim we employ the optimized RFADCC, adding a new one-step anti-CD14 and Live/dead staining. Combining flow cytometry and high-resolution confocal microscopy, we were able to follow the movement of fragments of membrane from the targets to the effectors, specifically to monocytes. Particularly, in the presence of monoclonal IgGs specific for Cluster A epitopes (A32 and C11) exposed on HIV-1 envelope, we were able to visualize the formation of stable immune synapses that include a Ba-L gp120-coated target and one or multiple monocytes. During the interaction, the whole immune complex, formed by Ba-L gp120 Ag and IgG, migrated and clustered towards the points of contact with monocyte(s) and transferred onto the surface of the effectors by trogocytosis. This phenomenon is very fast and it is strictly dependent on the formation of stable immunological synapses between HIV-1 sensitized cells and monocytes, since trogocytosis is not observed in the case of Synagis, which lacks its specific antigen and, in turns the ability of bridging Targets and Effectors. These findings support a new role for monocytes, potentially being the mediators of a new mechanism for clearance of viral antigens from target cells or potentially being new targets for the immune response against the virus after the acquisition viral IC from HIV-1 sensitized cells.
The Potential Role of CD133 in Immune Surveillance and Apoptosis: A Mitochondrial Connection? (2011)

High level of expression of CD133 may be a useful marker of more aggressive tumors that are recalcitrant toward established therapies. Compelling preliminary data indicate that drugs targeting mitochondria may be utilized as a novel, efficient cancer therapeutic modality.
Injectable Hydrogels by Enzymatic Co‐Crosslinking of Dextran and Hyaluronic Acid Tyramine Conjugates (2011)

Abstract In this study, injectable hydrogels were prepared by the horseradish peroxidase mediated co‐crosslinking of dextran‐tyramine (Dex‐TA) and hyaluronic acid‐tyramine (HA‐TA) conjugates intended for cartilage tissue engineering. In general the gelation times of 10 wt% polysaccharide solutions are &lt; 20 seconds and their storage moduli can be adjusted by varying the composition between Dex‐TA and HA‐TA. Dex‐TA/HA‐TA (50/50) hydrogels were fully degradable in the presence of hyaluronidase. Chondrocytes incorporated in 10 wt% Dex‐TA and Dex‐TA/HA‐TA (50/50) gels showed good viability after 28 days. These results indicate that Dex‐TA/HA‐TA (50/50) hydrogels are promising injectable and biodegradable hydrogels for cartilage repair.
A study on the UWB BPF using the hairpin-type LPF and the Parallel-coupled Lines (2009)

A compact ultra wide-band bandpass filter is proposed in this paper. The BPF consists of a hairpin-type LPF with a chip capacitor and a HPF using parallel-coupled lines. Firstly, the circuit model of LPF is investigated. Next, the characteristics of the HPF is also examined, and the results show the broad bandpass characteristics. Then the performances of UWB BPF composed of the LPF and the HPF are simulated and measured. As the results, the filter show the performance close to the FCC-full band. In addition, UWB BPF using high dielectric rod by LTCC technology is simulated which has the similar performance without the chip capacitor.
Quality of periodontal healing. IV: Enzyme histochemical evidence for an osteoblast origin of reparative cementum. (1994)

The aim of the present study was to map the distribution of healing gingival and periodontal connective tissue well as osteoblastic activity in marginal periodontal wound healing using activity of alkaline phosphatases as markers. Activity of non-specific alkaline phosphatase (NSAP) was abundant in periodontal but not in gingival connective tissue. Activity of vanadate-resistant alkaline phosphatase (VRAP) had a preferential localisation to periosteal and endosteal bone surfaces but was not detectable in cementoblasts along root surfaces. However, following spontaneous marginal healing of exposed dentine surfaces, activity of VRAP was also found on healing dentine surfaces. It was concluded that osteoblasts rather than cementoblasts form reparative cementum on exposed dentine surfaces during marginal periodontal healing.
Coding for the &amp;#x2113;&lt;inf&gt;&amp;#x221E;&lt;/inf&gt;-limited permutation channel (2015)

In this work we consider the communication of information in the presence of synchronization errors. Specifically, we consider permutation channels in which a transmitted codeword x = (x <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> , ..., x <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sub> ) is corrupted by a permutation π ∈ S <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sub> to yield the received word y = (y <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> , ..., y <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sub> ) where y <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">i</sub> = x <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">π(i)</sub> . We initiate the study of worst case (or zero error) communication over permutation channels that distort the information by applying permutations π which are limited to displacing any symbol by at most r locations, i.e. permutations π with weight at most r in the ℓ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">∞</sub> -metric. We present direct and recursive constructions, as well as bounds on the rate of such channels for binary and general alphabets. Specific attention is given to the case of r = 1.
Evolving Concepts in the Pathology and Computed Tomography Imaging of Lung Adenocarcinoma and Bronchioloalveolar Carcinoma (2005)

There is a need to work toward a mutual understanding and consensus between pathologists, clinicians, and researchers with the use of the term BAC versus adenocarcinoma. Future studies should make some attempt to quantitate these components and/or other features such as size of scar, size of invasive component, or pattern of invasion. Hopefully, this work will allow definition of a category of adenocarcinoma, mixed subtype with predominant BAC/minimal invasion and a favorable prognosis.
Computing the Girth of a Planar Graph in $O(n \logn)$ Time (2010)

We give an $O(n\log n)$ algorithm for computing the girth (shortest cycle) of an undirected n-vertex planar graph. Our solution extends to any graph of bounded genus. This improves upon the best previously known algorithms for this problem.
Don't Judge a Book by Its Cover (2011)

Kang et al 1 compare intravascular ultrasound (IVUS) parameters against a gold standard of fractional flow reserve (FFR) for evaluating intermediate stenoses. Their work adds another piece of evidence to a debate whose outcome is fundamentally changing interventional cardiology. As encapsulated by the title of the "FFR versus Angiography for Multivessel Evaluation" (FAME) trial, 2 the debate can be summarized simply: physiology versus anatomy. Its urgency and importance cannot be more clear, given recent skepticism toward the value of percutaneous coronary intervention (PCI): its ranking as 1 of the 10 most overused procedures in a consumer report 3 ; litigation against an interventional cardiologist for allegedly implanting inappropriate stents 4 ; and an editorial in a prominent medical journal calling to end ad hoc PCI. 5 Therefore, the work by Kang et al 1 is both timely and relevant.
Wave-pipelining: a tutorial and research survey (1998)

Wave-pipelining is a method of high-performance circuit design which implements pipelining in logic without the use of intermediate latches or registers. The combination of high-performance integrated circuit (IC) technologies, pipelined architectures, and sophisticated computer-aided design (CAD) tools has converted wave-pipelining from a theoretical oddity into a realistic, although challenging, VLSI design method. This paper presents a tutorial of the principles of wave-pipelining and a survey of wave-pipelined VLSI chips and CAD tools for the synthesis and analysis of wave-pipelined circuits.
Activation and Deactivation of DNAzyme and Antisense Function with Light for the Photochemical Regulation of Gene Expression in Mammalian Cells (2010)

The photochemical regulation of biological systems represents a very precise means of achieving high-resolution control over gene expression in both a spatial and a temporal fashion. DNAzymes are enzymatically active deoxyoligonucleotides that enable the site-specific cleavage of RNA and have been used in a variety of in vitro applications. We have previously reported the photochemical activation of DNAzymes and antisense agents through the preparation of a caged DNA phosphoramidite and its site-specific incorporation into oligonucleotides. The presence of the caging group disrupts either DNA:RNA hybridization or catalytic activity until removed via a brief irradiation with UV light. Here, we are expanding this concept by investigating the photochemical deactivation of DNAzymes and antisense agents. Moreover, we report the application of light-activated and light-deactivated antisense agents to the regulation of gene function in mammalian cells. This represents the first example of gene silencing antisense agents that can be turned on and turned off in mammalian tissue culture.
Bulk and surface recombination properties in thin film semiconductors with different surface treatments from time-resolved photoluminescence measurements (2019)

The knowledge of minority carrier lifetime of a semiconductor is important for the assessment of its quality and design of electronic devices. Time-resolved photoluminescence (TRPL) measurements offer the possibility to extract effective lifetimes in the nanosecond range. However, it is difficult to discriminate between surface and bulk recombination and consequently the bulk properties of the semiconductor cannot be estimated reliably. Here we present an approach to constrain systematically the bulk and surface recombination parameters in semiconducting layers and reduces to finding the roots of a mathematical function. This method disentangles the bulk and surface recombination based on TRPL decay times of samples with different surface preparations. The technique is exemplarily applied to a CuInSe<sub>2</sub> and a back-graded Cu(In,Ga)Se<sub>2</sub> compound semiconductor, and upper and lower bounds for the recombination parameters and the mobility are obtained. Sets of calculated parameters are extracted and used as input for simulations of photoluminescence transients, yielding a good match to experimental data and validating the effectiveness of the methodology. A script for the simulation of TRPL transients is provided.
Hydrogen Lyman α coronagraph/polarimeter (1992)

The present treatment of vector magnetic field measurement in coronas by means of the Hanle effect of the Lyman-alpha line uses data from all-reflecting imaging coronagraph/polarimeters. The polarization sensitivity, bandpass, and spatial resolution of these instruments are defined through a modeling of the Hanle-effect signature in Lyman-alpha emission from coronal magnetic loops; the line-of-sight integration through an inhomogeneous coronal medium is taken into account. The use of the Hanle effect to measure solar corona vector magnetic fields is verified.
EL RESUMEN. EVALUACIÓN DE LA COMPRENSIÓN LECTORA EN ESTUDIANTES UNIVERSITARIOS ASSESSMENT OF READING COMPREHENSION IN UNDERGRADUATE STUDENTS: THE SUMMARY (2005)

The aim of this study was to assess the relationship be tween summary production and type of text. Summary production implies building a concise and comprehen sive representation of the original text (Kintsch & van Dijk, 1975). Previous research has shown the influence of type of text (expositive vs. narrative) in text compre hension (Meyer, 1984; Mc Namara, 2004). In this study, a total of 83 undergraduate students read a narrative and an expository text and later summarized them. Each summary was scored into two scales: content and co herence, and was classified according to its structural organization. Results indicate different scores among scales, with a better performance in content, and show
Efﬁciency of T4 Gene 60 Translational Bypassing (1998)

Ribosomes translating bacteriophage T4 gene 60 mRNA bypass 50 noncoding nucleotides from a takeoff site\n\t\t\t\t at codon 46 to a landing site just upstream of codon 47. A key signal for efficient bypassing is contained within\n\t\t\t\t the nascent peptide synthesized prior to takeoff. Here we show that this signal is insensitive to the addition of\n\t\t\t\t coding information at its N terminus. In addition, analysis of amino-terminal fusions, which allow detection of\n\t\t\t\t all major products synthesized from the gene 60 mRNA, show that 50% of ribosomes bypass the coding gap\n\t\t\t\t while the rest either terminate at a UAG stop codon immediately following codon 46 or fail to resume coding.\n\t\t\t\t Bypassing efficiency estimates significantly lower than 50% were obtained with enzymatic reporter systems that\n\t\t\t\t relied on comparing test constructs to constructs with a precise excision of the gap (gap deletion). Further\n\t\t\t\t analysis showed that these estimates are distorted by differences between test and gap deletion functional\n\t\t\t\t mRNA levels. An internal translation initiation site at Met12 of gene 60 (which eliminates part of the essential\n\t\t\t\t nascent peptide) also distorts these estimates. Together, these results support an efficiency estimate of ~50%,\n\t\t\t\t less than previously reported. This estimate suggests that bypassing efficiency is determined by the competition\n\t\t\t\t between reading signals and release factors and gives new insight into the kinetics of bypassing signal action.
Analysis of PhaseLocked Timing Extraction Circuits for Pulse Code Transmission (2009)

An analysis is presented of the performance of phaselocked timing extraction circuits for baseband pulse code transmission. The phase error of the extracted timing wave is influenced by the properties of three essential stages in signal processing: prefiltering, nonlinear treatment, and narrow-band filtering. The analysis enables us to calculate quantitatively the quasi-static and the dynamic part of the phase error for arbitrary but specified types of signal processing. This is more than can be done with existing theory in the case of resonant-type timing extraction circuits. Examples are given for practical cases, and conditions for optimum performance are derived. Furthermore, the behavior of such phase-locked circuits in a chain of repeaters is investigated, and in particular, the propagation law for jitter. Byrne's model, as used for resonant-type timing extraction circuits, therefore is generalized. It is shown analytically and experimentally that by proper implementation of the timing extraction circuit, considerable improvement can be obtained as compared with resonant-type circuits.
PCH1 regulates light, temperature, and circadian signaling as a structural component of phytochrome B-photobodies in <i>Arabidopsis</i> (2019)

The members of the phytochrome (phy) family of bilin-containing photoreceptors are major regulators of plant photomorphogenesis through their unique ability to photointerconvert between a biologically inactive red light-absorbing Pr state and an active far-red light-absorbing Pfr state. While the initial steps in Pfr signaling are unclear, an early event for the phyB isoform after photoconversion is its redistribution from the cytoplasm into subnuclear foci known as photobodies (PBs), which dissipate after Pfr reverts back to Pr by far-red irradiation or by temperature-dependent nonphotochemical reversion. Here we present evidence that PHOTOPERIODIC CONTROL OF HYPOCOTYL 1 (PCH1) functions both as an essential structural component of phyB-containing PBs and as a direct regulator of thermal reversion that is sufficient to stabilize phyB as Pfr in vitro. By examining the genetic interaction between a constitutively active phyB<sup>Y276H</sup>-YFP allele (<i>YHB-YFP</i>) and PCH1, we show that the loss of PCH1 prevents YHB from coalescing into PBs without affecting its nuclear localization, whereas overexpression of PCH1 dramatically increases PB levels. Loss of PCH1, presumably by impacting phyB-PB assembly, compromises a number of events elicited in <i>YHB-YFP</i> plants, including their constitutive photomorphogenic phenotype, red light-regulated thermomorphogenesis, and input of phyB into the circadian clock. Conversely, elevated levels of both phyB and PCH1 generate stable, yet far-red light-reversible PBs that persisted for days. Collectively, our data demonstrate that the assembly of PCH1-containing PBs is critical for phyB signaling to multiple outputs and suggest that altering PB dynamics could be exploited to modulate plant responses to light and temperature.
Phase selective synthesis of nickel silicide nanocrystals in molten salts for electrocatalysis of the oxygen evolution reaction (2020)

We report phase selective synthesis of intermetallic nickel silicide nanocrystals in inorganic molten salts. NiSi and Ni2Si nanocrystals are obtained by reacting a nickel(ii) salt and sodium silicide Na4Si4 in the molten LiI-KI inorganic eutectic salt mixture. We report that nickel silicide nanocrystals are precursors to active electrocatalysts in the oxygen evolution reaction (OER) and may be low-cost alternatives to iridium-based electrocatalysts.