gebhart/patrepeval huggingface dataset:
Structural Studies on Hydrogen‐Bonding Receptors for Barbiturate Guests That Use Metal Ions as Allosteric Inhibitors (2003)

Abstract Receptor 1 was designed to bind barbiturate substrates through a six‐point hydrogen‐bonding motif only in the absence of metal allosteric cofactors. It was predicted that the binding of metal ions by bipyridine ligands in 1 would result in a geometric change in the receptor to inhibit substrate recognition. However, receptor 1 showed minimal affinity for the barbiturate guests even in the absence of the metal. Binding studies on model compounds 2 , 3 , 5 , and 6 revealed that the inactivity of 1 is due to an intramolecular hydrogen bond between the N−H donor groups and the nitrogen atoms on the first heterocycle of the bipyridine ligands. This intramolecular hydrogen‐bonding was eliminated by altering the position of the tether between the bipyridine ligands and the active site to produce receptor 7 . Consequently, the high affinity exhibited by 7 for the barbiturate substrate ( K a = 2.8±0.7 × 10 3 M −1 in 9:1 CD 2 Cl 2 /CD 3 CN) was significantly reduced by the addition of Zn II ions as a negative allosteric co‐factor. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004)
Pharmacokinetics and tissue disposition of urolithin A, an ellagitannin‐derived metabolite, in mice (2007)

Ellagitannins (ETs) are bioactive polyphenols present in some fruits (pomegranates, strawberries, red and black raspberries) and nuts (almonds, walnuts). Once consumed, ETs hydrolyze and are absorbed as ellagic acid which rapidly clears from plasma over 5 h. Ellagic acid is further metabolized by liver enzymes and gut microflora into 1,6-hydroxybenzopyran derivatives (or urolithins). However the pharmacokinetics and tissue disposition of urolithins has not been reported. Therefore we synthesized and intraperitoneally (i.p.) or orally administered urolithin A (UA) to B6 mice. Blood (over 24 h) and tissues (prostate, liver, kidney, lung, colon, intestine, brain) were collected and analyzed for UA and its conjugates by high performance liquid chromatography mass spectrometry. Metabolite levels were UA >UA-sulphate>UA-glucuronide>methylated-UA; all metabolites cleared by 24 h. UA concentration was highest in mouse prostate tissues by the oral route, and in colon and prostate tissues by the i.p. route. Only methlyated-UA was detected in brain tissues. Administration by i.p. resulted in shorter Tmax (2 h) and higher concentrations than oral administration (Tmax, 4 h). Given that the mouse prostate gland was a main target tissue of concentration by UA, and the previous report of the effects of pomegranate juice on prostate cancer patients, further human bioavailability studies are warranted.
Hemicatenanes form upon inhibition of DNA replication (2000)

Plasmid DNA incubated in interphase Xenopus egg extracts is normally assembled into chromatin and then into synthetic nuclei which undergo one round of regulated replication. During a study of restriction endonuclease cut plasmid replication intermediates (RIs) by the Brewer-Fangman 2D gel electrophoresis technique, we have observed the formation of a strong spike of X-shaped DNA molecules in extracts that otherwise yield very little or no RIs. Formation of these joint molecules is also efficiently induced in replication-competent extracts upon inhibition of replication fork progression by aphidicolin. Although their electrophoretic properties are quite similar to those of Holliday junctions, 2D gels of doubly cut plasmids show that these junctions can link two plasmid molecules at any pair of DNA sequences, with no regard for sequence homology at the branch points. Neutral-neutral-alkaline 3D gels show that the junctions only contain single strands of parental size and no recombinant strands. A hemicatenane, in which one strand of a duplex is wound around one strand of another duplex, is the most likely structure to account for these observations. The mechanism of formation of these novel joint DNA molecules and their biological implications are discussed.
High Performance Flexible Piezoelectric Nanogenerators based on BaTiO<sub>3</sub> Nanofibers in Different Alignment Modes (2016)

Piezoelectric nanogenerators, harvesting energy from mechanical stimuli in our living environments, hold great promise to power sustainable self-sufficient micro/nanosystems and mobile/portable electronics. BaTiO3 as a lead-free material with high piezoelectric coefficient and dielectric constant has been widely examined to realize nanogenerators, capacitors, sensors, etc. In this study, polydimethylsiloxane (PDMS)-based flexible composites including BaTiO3 nanofibers with different alignment modes were manufactured and their piezoelectric performance was examined. For the study, BaTiO3 nanofibers were prepared by an electrospinning technique utilizing a sol-gel precursor and following calcination process, and they were then aligned vertically or horizontally or randomly in PDMS matrix-based nanogenerators. The morphological structures of BaTiO3 nanofibers and their nanogenerators were analyzed by using SEM images. The crystal structures of the nanogenerators before and after poling were characterized by X-ray diffraction. The dielectric and piezoelectric properties of the nanogenerators were investigated as a function of the nanofiber alignment mode. The nanogenerator with BaTiO3 nanofibers aligned vertically in the PDMS matrix sheet achieved high piezoelectric performance of an output power of 0.1841 μW with maximum voltage of 2.67 V and current of 261.40 nA under a low mechanical stress of 0.002 MPa, in addition to a high dielectric constant of 40.23 at 100 Hz. The harvested energy could thus power a commercial LED directly or be stored into capacitors after rectification.
Biological implications of bi-directional fetomaternal cell traffic: a summary of a National Institute of Child Health and Human Development-sponsored conference (2003)

Objective: The National Institute of Child Health and Human Development (NICHD) held a workshop on 27-28 July 2000 to bring together investigators working in the field of fetomaternal cellular and nucleic acid trafficking with the hope that this would stimulate further research into the biological implications of such phenomena. Methods: Invited speakers from all over the world presented their latest (unpublished) data. The conference proceedings were delayed until the present time to allow independent publication of the primary data. Results and conclusions: Bi-directional fetomaternal trafficking of cells and nucleic acids during pregnancy is now well established, through the use of molecular techniques including conventional and real-time polymerase chain reaction, as well as fluorescence in situ hybridization. In addition, human leukocyte antigen (HLA) is deposited in the skin of pregnant women. Feto-maternal trafficking is increased in some complications of pregnancy, such as pre-eclampsia, polyhydramnios, polymorphic eruption of pregnancy, preterm labor and specific fetal chromosome aneuploidies. Maternal cells and nucleic acids have been documented in umbilical cord blood and in autopsy tissue of non-transfused neonates. Fetal cells persist postpartum and may be associated with the development of disorders such as scleroderma, lichen planus, lupus and thyroid disease. The extent of fetomaternal trafficking may be affected by three generational HLA relationships. Thus, the consequences of pregnancy extend beyond gestation.
A new direction in integrated circuit technology (2007)

Many people worry about the future of IC technology, since the effect of technology scaling has been saturated. We should change our way of thinking. A saturation of process technology will induce emergences of new design technologies, new integration technologies, and new application areas. Digital system design will adopt high throughput architectures to realize higher processing throughput, even if the clock frequency has saturated. Utilization of multi-core design, parallel processing, and dedicated processing engines used in video processors will increase. Three-dimensional integration technology will be employed to shorten the interconnection delay and to realize real integrated systems that need heterogeneous device integration. Millimeter wave SoC will realize several Gbps wireless communication. The wavelength will be comparable to the length of elements on a chip and the use of transmission lines and on-chip antennas will be feasible. New circuit technology that can address EM control will work on a chip such as phased array antenna systems. Micro power technology will emerge to control and transmit electrical power.
Analysis of the Survivability of GaN Low-Noise Amplifiers (2007)

This paper presents a detailed analysis of the stressing mechanisms for highly rugged low-noise GaN monolithic-microwave integrated-circuit amplifiers operated at extremely high input powers. As an example, a low-noise amplifier (LNA) operating in the 3-7-GHz frequency band is used. A noise figure (NF) below 2.3 dB is measured from 3.5 to 7 GHz with NF<1.8 dB between 5-7 GHz. This device survived 33 dBm of available RF input power for 16 h without any change in low-noise performance. The stress mechanisms at high input powers are identified by systematic measurements of an LNA and a single high electron-mobility transistor in the frequency and time domains. It is shown that the gate dc current, which occurs due to self-biasing, is the most critical factor regarding survivability. A series resistance in the gate dc feed can reduce this gate current by feedback, and may be used to improve LNA ruggedness
<sup>23</sup>Na MRI accurately measures fixed charge density in articular cartilage (2002)

One of the initiating steps of osteoarthritis is the loss of proteoglycan (PG) molecules from the cartilage matrix. One method for assessing cartilage integrity, therefore, is to measure the PG content or fixed charge density (FCD) of cartilage. This report shows the feasibility of calculating FCD by (23)Na MRI and introduces MRI protocols for human studies, in vivo. (23)Na MRI was used to measure the sodium concentration inside bovine patellar cartilage. The sodium concentration was then converted to FCD (mM) by considering ideal Donnan equilibrium. These FCD measurements were compared to FCD measurements obtained through standard dimethylmethylene blue PG assays. There was a high correlation (slope = 0.89, r(2) = 0.81) between the FCD measurements obtained by (23)Na MRI and those obtained by the PG assays. These methods were then employed in quantifying the FCD of articular cartilage of human volunteers in vivo. Two imaging protocols were compared: one using a birdcage coil, the other using a transmit/receive surface coil. Both methodologies gave similar results, with the average sodium concentration of normal human patellar cartilage ranging from approximately 240 to 260 mM. This corresponds to FCDs of -158 mM to -182 mM.
Sputtered thermocouple for lyophilization monitoring (2012)

This paper describes development and characterization of thin film thermocouples to be used as a non-perturbating solution to follow the freeze-drying process of pharmaceutical chemicals. Pharmaceutical chemicals are routinely produced by means of freeze-dryers with excellent results, however the drying process is slow requiring days to complete and this increases the product cost. To optimize the process, reducing the drying time, this must be carried out close to the maximum allowed temperature. A monitoring system able to continuously monitor the product temperature during the drying could greatly reduce the damage risk, but actual sensors are too invasive to permit a reliable measurement and radiation remote systems cannot be used. This paper describes the results obtained by developing thermocouples with sub-micrometric thickness which can be embedded into the vial walls without significatively altering the wall thickness and properties. Prototypes of the proposed thermocouples have been realized and successfully tested.
Theiler's murine encephalomyelitis virus (TMEV)-induced demyelinating disease in mice is influenced by the H-2D region: correlation with TEMV-specific delayed-type hypersensitivity. (1985)

Intracranial inoculation of Theiler's murine encephalomyelitis virus (TMEV) leads to the development of a chronic demyelinating disorder in certain mouse strains. Development of this disease is controlled by at least two unlinked genes, one of which is within or linked to the H-2 complex. In the present study, we attempted to map the relevant H-2 loci involved in susceptibility to TMEV-induced demyelination using crosses between SJL and several congenic H-2 recombinant mouse strains bearing different combinations of MHC genes from the susceptible H-2s and resistant H-2b haplotypes all on the C57BL/10 strain background. The data suggest that the D region of the H-2 complex strongly influences development of the demyelinating disease because increased susceptibility correlates well with homozygosity for H-2s alleles in the D region, but not in K or I-A. In addition, we also attempted to correlate certain immune and nonimmune pathophysiologic parameters with the development of clinical disease. Specifically, central nervous system TMEV titers and TMEV-specific humoral and cellular [delayed-type hypersensitivity (DTH) and T cell proliferative (Tprlf)] responses were examined. The data show that TMEV-induced demyelinating disease did not correlate with either CNS TMEV titers or TMEV-specific humoral or Tprlf responses but did correlate closely with the presence of high levels of TMEV-specific DTH. Collectively, our findings demonstrating a strong correlation between disease incidence, the presence of particular H-2D region genotypes, and high levels of TMEV-specific DTH in susceptible strains (as well as previous findings showing predominant mononuclear cell infiltrates in CNS demyelinating lesions) support the hypothesis that the disease is immune mediated rather than a result of direct cytolytic effects of virus infection.
Thermal and Photocatalytic Degradation of Poly(methyl methacrylate), Poly(butyl methacrylate), and Their Copolymers (2008)

The photocatalytic degradation of the homopolymers, poly(methyl methacrylate) (PMMA), poly(butyl methacrylate) (PBMA), and their copolymers (PMMABMA) was studied in o-dichlorobenzene in the presence of commercial TiO2 (Degussa P-25) and TiO2 synthesized by combustion synthesis (CSN-TiO2). Gel permeation chromatography was used to determine the evolution of molecular weight distributions with reaction time. The experimental data indicated that the polymers PMMA and PBMA and their copolymers degrade by simultaneous random and chain end scission. A continuous distribution model was developed for the mechanism involved in degradation by both random and chain end scission and used to determine the degradation rate coefficients. The degradation rate coefficients of the polymers in the presence of CSN-TiO2 were higher than the degradation rate coefficients obtained with commercial TiO2 (Degussa P-25). The degradation rate coefficient of copolymers was in between that of the homopolymers and increased linearly with the increase of mol % of PMMA. The degradation of PMMA, PBMA, and their copolymers was also investigated by thermogravimetric analysis. The copolymers exhibited better thermal stability than the homopolymers in contrast to that observed for photocatalytic degradation.
Unsupervised textured image segmentation (1992)

A new algorithm for unsupervised textured image segmentation is presented. The image comprises M textured regions, each of which is modeled by a stationary Gaussian Markov random field. A feature vector is computed for each pixel in the original image where these vectors are normally distributed and cluster about some vector means. Thus, the problem is reduced to one of restoring a vector valued underlying field embedded in additive Gaussian noise. The vector means corresponding to the different regions are estimated by using the expectation-maximization (EM) algorithm. An iterative algorithm is used with the underlying field modeled as a multilevel logistic Markov random field. The results obtained on two-region and four-region textured images are impressive, and the classification error is less than 3%. The algorithm is not limited to textured images but can also be applied to any vector-valued signals.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
<i>In vitro</i> synthesis of the iron–molybdenum cofactor of nitrogenase from iron, sulfur, molybdenum, and homocitrate using purified proteins (2007)

Biological nitrogen fixation, the conversion of atmospheric N2 to NH3, is an essential process in the global biogeochemical cycle of nitrogen that supports life on Earth. Most of the biological nitrogen fixation is catalyzed by the molybdenum nitrogenase, which contains at its active site one of the most complex metal cofactors known to date, the iron-molybdenum cofactor (FeMo-co). FeMo-co is composed of 7Fe, 9S, Mo, R-homocitrate, and one unidentified light atom. Here we demonstrate the complete in vitro synthesis of FeMo-co from Fe(2+), S(2-), MoO4(2-), and R-homocitrate using only purified Nif proteins. This synthesis provides direct biochemical support to the current model of FeMo-co biosynthesis. A minimal in vitro system, containing NifB, NifEN, and NifH proteins, together with Fe(2+), S(2-), MoO4(2-), R-homocitrate, S-adenosyl methionine, and Mg-ATP, is sufficient for the synthesis of FeMo-co and the activation of apo-dinitrogenase under anaerobic-reducing conditions. This in vitro system also provides a biochemical approach to further study the function of accessory proteins involved in nitrogenase maturation (as shown here for NifX and NafY). The significance of these findings in the understanding of the complete FeMo-co biosynthetic pathway and in the study of other complex Fe-S cluster biosyntheses is discussed.
Structural Basis of Plasticity in T Cell Receptor Recognition of a Self Peptide-MHC Antigen (1998)

The T cell receptor (TCR) inherently has dual specificity. T cells must recognize self-antigens in the thymus during maturation and then discriminate between foreign pathogens in the periphery. A molecular basis for this cross-reactivity is elucidated by the crystal structure of the alloreactive 2C TCR bound to self peptide-major histocompatibility complex (pMHC) antigen H-2Kb-dEV8 refined against anisotropic 3.0 angstrom resolution x-ray data. The interface between peptide and TCR exhibits extremely poor shape complementarity, and the TCR beta chain complementarity-determining region 3 (CDR3) has minimal interaction with the dEV8 peptide. Large conformational changes in three of the TCR CDR loops are induced upon binding, providing a mechanism of structural plasticity to accommodate a variety of different peptide antigens. Extensive TCR interaction with the pMHC alpha helices suggests a generalized orientation that is mediated by the Valpha domain of the TCR and rationalizes how TCRs can effectively "scan" different peptides bound within a large, low-affinity MHC structural framework for those that provide the slight additional kinetic stabilization required for signaling.
Nitrogenous chelate complexes of transition metals. V. Binuclear hydroxybridged copper(II) complexes of 1,10-phenanthroline and 2,2'-bipyridyl (1968)

A series of compounds of the type OH [chelate Cu ' \Cu chelate]X,,nH20 \OH/ [where chelate = 1,lO-phenanthroline; X = 01 (n = 3), Br (n = 4), I (n = 2), NCS (n = 2), C10, (n = 1); 2X = SO, (n = 5), PtCl, (n = 4), and where chelate = 22'-bipyridyl; X = C1 (n = 3), Br (n = 4), I (n = 3), NCS (n = l), PF6 (n = 2), C10, (n = 1); 2X = SO4 (n = 5) and PtC1, (n = 3)] have been prepared and their properties investigated. In dilute aqueous solution the compounds are ionized forming the solvated [chelate Cu(OH,)Cu chelateI2+ species which exhibit similar visible absorption spectra (where chelate = p,h, ,eAn, = 630 mp and 6 = 97, and where chelate = b ,i,p,Ay, = 620 mp and E = 105). In nitrobenzene solution some of these compounds have been shown from electrical conductivity and spectrophotometric measurements to involve coordination of the anion to the copper(11) atoms. This effect has also been verified in the solid state by the measurement of diffuse reflectance spectra. The compounds all exhibit room temperature magnetic moments of the order of 2.0 B.&I. per copper atom. A study of the magnetic susceptibility of the sulphate [bipy Cu(OH),Cu bipy]S04,5H,0 over the temperature range 83-293'~ showed no antiferromagnetic interaction between pairs of hydroxy-bridged copper atoms, and the results obey a Curie-Weiss law (8 -13'~). The average value of the corrected moment is 1.91 B.M. per copper atom. A value for g of 2.20 was estimated from these data, and is in agreement with the average g value of 2.19 obtained from an e.s.r. measurement.
Theoretical studies of minority carrier concentration profiles and cathodoluminescence intensities in thin-film materials with different surface recombination velocities and arbitrary excitation density (1992)

The authors consider a particular model of electron-beam-induced pair excitation. This model takes account of thickness dependence and is therefore considerably more realistic than the constant generation rate they assumed in a previous paper. The surface recombination velocity (SRV) on the upper surface can be varied independently of that on the lower surface. An exact analytical expression for the Green function (GF) has been found. Further, general expressions for the minority carrier concentration profile (MCCP), and hence for the cathodoluminescence intensity (CLI) are constructed merely by convolving the GF with the pair-generation function which is allowed to assume arbitrary form. Here a 'correlation function' form of the pair excitation density is considered which non-trivially makes the entire problem be of completely analytical formulation. The influence of various physical parameters, especially the SRV, the diffusion length (DL), and the incident voltage on the MCCP and CLI, are discussed in more detail theoretically and numerically. Explicit analytical forms of the GF, MCCP, and CLI are given for various surface-recombination conditions as well as expressions for junction current (JC) in the charge-collecting modes. An example is given of a model prediction in agreement with experimental results which cannot be obtained by previously existing models. It is found that the present formalism can also be used to tackle the problems of dislocation- or defect-imaging contrast and resolution in thin film materials within some approximation scheme and that many past models can be reproduced from the present model as special cases. It is anticipated that the generality of the model which the authors propose will be of considerable interest in seeking an understanding of experimental results. Quantitative calculations reveal many interesting and even unusual features contained in the new model.