gebhart/patrepeval huggingface dataset:
FRET from Multiple Pathways in Fluorophore-Labeled DNA (2016)

Because of their ease of design and assembly, DNA scaffolds provide a valuable means for organizing fluorophores into complex light harvesting antennae. However, as the size and complexity of the DNA–fluorophore network grows, it can be difficult to fully understand energy transfer properties because of the large number of dipolar interactions between fluorophores. Here, we investigate simple DNA–fluorophore networks that represent elements of the more complex networks and provide insight into the Förster Resonance Energy Transfer (FRET) processes in the presence of multiple pathways. These FRET networks consist of up to two Cy3 donor fluorophores and two Cy3.5 acceptor fluorophores that are linked to a rigid dual-rail DNA scaffold with short interfluorophore separation corresponding to 10 DNA base pairs (∼34 Å). This configuration results in five FRET pathways: four hetero-FRET and one homo-FRET pathway. The FRET properties are characterized using a combination of steady-state and time-resolved spectroscopy and understood using Förster theory. We show that the multiple FRET pathways lead to an increase in FRET efficiency, in part because homo-FRET between donor fluorophores provides access to parallel pathways to the acceptor and thereby compensates for low FRET efficiency channels caused by a static transition dipole distribution. More generally, the results show that multiple pathways may be used in the design of artificial light harvesting devices to compensate for inhomogeneities and nonideal ensemble effects that degrade FRET efficiency.
Two-Dimensional Mott-Hubbard Electrons in an Artificial Honeycomb Lattice (2011)

Artificial crystal lattices can be used to tune repulsive Coulomb interactions between electrons. We trapped electrons, confined as a two-dimensional gas in a gallium arsenide quantum well, in a nanofabricated lattice with honeycomb geometry. We probed the excitation spectrum in a magnetic field, identifying collective modes that emerged from the Coulomb interaction in the artificial lattice, as predicted by the Mott-Hubbard model. These observations allow us to determine the Hubbard gap and suggest the existence of a Coulomb-driven ground state.
The vector apodizing phase plate coronagraph: prototyping, characterization and outlook (2014)

The Apodizing Phase Plate (APP) is a phase-only pupil-plane coronagraph that suppresses starlight in a D-shaped region from 2 to 7 λ D around a target star. Its performance is insensitive to residual tip-tilt variations from the AO system and telescope structure. Using liquid crystal technology we develop a novel and improved version of the APP: the broadband vector Apodizing Phase Plate (vAPP). The vAPP prototype consists of an achromatic half-wave retarder pattern with a varying fast axis encoding phase structure down to 25 microns. The fast axis encodes the required phase pattern through the vector phase, while multiple twisting liquid crystal layers produce a nearly constant half-wave retardance over a broad bandwidth. Since pupil phase patterns are commonly designed to be antisymmetric, two complementary PSFs are produced with dark holes on opposite sides. We summarize results of the characterization of our latest vAPP prototype in terms of pupil phase reconstruction and PSF contrast performance. The liquid crystal patterning technique allows us to manufacture more extreme phase patterns than was possible before. We consider phase-only patterns that yield higher contrasts and better inner working angles than previous APPs, and patterns that produce dark regions 360 degrees around the PSF core. The possibility of including a phase ramp into the coronagraph is demonstrated, which simplifies the vAPP into a single optic. This additional phase ramp removes the need for a quarter-wave plate and a Wollaston prism, and enables the simplified implementation of a vAPP in a filter wheel at a pupil-plane location. Since the phase ramp is analogous to a polarization grating, it generates a (polarized) spectrum of a planet inside the dark hole, and thus allows for instantaneous characterization of the planet.
El acogimiento en familia ajena en España. Una evaluación de la práctica y sus resultados (2010)

ResumenEl acogimiento familiar ha de ser la medida prioritaria para los casos de menores que deben ser separados de su familia por motivos de protección. En España es una alternativa que cuenta tan sólo con veinte años de existencia y hasta la fecha no existen prácticamente datos acerca del grado de su implantación y sus características cuando se trata de acogimiento en familia ajena, mientras que son varios los trabajos que han estudiado el acogimiento en familia extensa. Este artículo presenta por primera vez en la literatura científica los datos más relevantes que permiten caracterizar la práctica del acogimiento en familia ajena en España, mediante el estudio de una muestra de seis comunidades autónomas bien representativas, con un total de 357 casos. El artículo presenta los perfiles de los niños, las familias biológicas y acogedoras, el proceso y algunos resultados sobre una submuestra de casos cerrados (n = 179). Se analizarán algunas características especialmente importantes como la larga estancia y la estabilidad de estos acogimientos, que los diferencia de los realizados en otros países.
Shape‐Dependent Targeting of Injured Blood Vessels by Peptide Amphiphile Supramolecular Nanostructures (2015)

Targeting of vascular intervention by systemically delivered supramolecular nanofibers after balloon angioplasty is described. Tracking of self-assembling peptide amphiphiles using fluorescence shows selective binding to the site of vascular intervention. Cylindrical nanostructures are observed to target the site of arterial injury, while spherical nanostructures with an equivalent diameter display no binding.
To culture or not to culture: fecal lactoferrin screening for inflammatory bacterial diarrhea (1996)

Because of its low yield in unselected specimens, stool culture is often cost ineffective. We tested 55 fecal samples from Fairfax Hospital (46 patients with diarrhea and 9 from controls without diarrhea) for lactoferrin by latex agglutination (LFLA) with the Leukotest (Techlab, Blacksburg, Va.) as a marker for inflammatory diarrhea. Of the 28 samples with Salmonella, Shigella, or Campylobacter infection, 93% had detectable fecal lactoferrin at > or = 1:50 (61% had LFLA titers of > or = 1:400), while 83% of 18 samples with rotavirus or no detectable pathogen were LFLA negative at a titer of 1:50 (100% were negative at 1:400). All 9 controls without diarrhea were LFLA negative at 1:50. The use of fecal lactoferrin to screen for inflammatory diarrhea selects specimens for which stool culture is fivefold more likely to yield an invasive bacterial pathogen (reducing the cost per positive result by over $800) and thus may greatly enhance a cost-effective approach to evaluating diarrheal illness.
Use of cyclooxygenase-2 inhibition to enhance the efficacy of immunotherapy. (2003)

Antitumor effects of cyclooxygenase-2 (COX-2) inhibition have been reported in a wide variety of tumor models and in human cancers, both as chemoprevention and therapy. Human mesothelioma tumors have been shown to overexpress COX-2 and high levels of COX-2 protein have been demonstrated to be a prognostic factor, indicating poor outcome in this tumor. In this study, we determined that inhibition of COX-2 by oral administration of Rofecoxib significantly slowed but did not cure the growth of small tumors in mesothelioma-bearing mice. Large tumors were unaffected. This effect was dependent on the presence of CD8+ T cells and was associated with increased tumor-infiltrating lymphocytes. Because these activities are consistent with a mechanism that results in a decrease in the immunosuppressive environment of the tumor, we additionally examined the effect of COX-2 blockade combined with Ad.IFN-beta therapy, a treatment that we have previously demonstrated results in expansion of antitumor CD8+ CTLs and cures a high percentage of small mesothelioma tumors in mice. Ad.IFN-beta therapy combined with COX-2 inhibition was associated with an increased number of T cells within tumors and resulted in cures of small tumors, significant inhibition of the growth of large established tumors, and inhibition of the growth of metastatic tumor foci after surgical debulking. The additive effects of these modes of treatment suggests that it would be rational to combine COX-2 inhibition with immuno- and immunogene therapy approaches (perhaps in conjunction with surgical debulking) in human clinical trials of treatment of mesothelioma and other tumors.
ChemInform Abstract: Acidity Characterization of Heterogeneous Catalysts by Solid‐State NMR Spectroscopy Using Probe Molecules (2014)

Abstract Review: 80 refs.
Synthetic peptide substrates for the immunoglobulin A1 protease from Neisseria gonorrhoeae (type 2) (1991)

Neisseria gonorrhoeae secretes protease which inactive human immunoglobulin A1 (IgA1) by cleavage of specific peptide bonds in the hinge region. The type 2 IgA1 protease (EC 3.4.24.13) is secreted as a 169-kDa precursor which undergoes autoproteolysis at three sites (A, B, and C) to release the 106-kDa active form of the enzyme (J. Pohlner, R. Halter, K. Beyreuther, and T. F. Meyer. Nature [London] 325:458-462, 1987). Synthetic decapeptides consisting of five residues on each side of the three autoproteolytic cleavage sites and their potential pentapeptide catabolites were prepared by solid-phase synthesis. Cleavage of the decapeptides by the type 2 IgA1 protease from N. gonorrhoeae was monitored by high-performance liquid chromatography. Peptides homologous with the amino acid sequences around the B and C sites are cleaved by the IgA1 protease. Amino acid analysis and Edman degradation show that the cleavage products have both the composition and amino acid sequence which would be expected from cleavage at the predicted sites. Km values of 1.35 mM and 3.43 mM and kcat values of 280 pmol/h/U and 439 pmol/h/U for the site B and site C peptides, respectively, were determined. The catalytic efficiency (kcat/Km) for the synthetic substrates is about 10% of that reported for intact IgA1. Cleavage of the peptides is inhibited by IgA1 protease inhibitors such as the tetrapeptide substrate analog inhibitor HRP-48, human colostrum, and a peptide-boronate transition state inhibitor. An extract from an N. gonorrhoeae construct lacking active IgA1 protease failed to cleave the synthetic substrate, while an extract from the control construct which secretes active enzyme completely hydrolyzed the synthetic peptide. Neither the site A peptide nor synthetic decapeptides encompassing cleavage sites in the hinge region of IgA1 are hydrolyzed by IgA1 protease. These are the first synthetic substrates to be reported for any IgA1 protease.
Genetic studies reveal that myristoylCoA:protein N‐myristoyltransferase is an essential enzyme in <i>Candida albicans</i> (1995)

MyristoylCoA:protein N-myristoyltransferase (Nmt) catalyses the co-translational, covalent attachment of myristate (C14:0) to the amino-terminal glycine residue of a number of eukaryotic proteins involved in cellular growth and signal transduction. The NMT1 gene is essential for vegetative growth of Saccharomyces cerevisiae. Studies were carried out to determine if Nmt is also essential for vegetative growth of the pathogenic fungus Candida albicans. A strain of C. albicans was constructed in which one copy of NMT was partially deleted and disrupted. A Gly-447-->Asp mutation was introduced into the second NMT allele. This mutation produced marked reductions in catalytic efficiency at 24 and 37 degrees C, as judged by in vitro kinetic studies of the wild-type and mutant enzymes which had been expressed in, and purified from, Escherichia coli. The growth characteristics of isogenic NMT/NMT, NMT/delta nmt, and nmt delta/nmtG447D C. albicans strains were assessed under a variety of conditions. Only the nmt delta/nmtG447D strain required myristate for growth. This was true at both 24 and 37 degrees C. Palmitate could not substitute for myristate. Incubation of nmt delta/nmtG447D cells at 37 degrees C in the absence of myristate resulted in cell death as observed by the inability to form colonies on media supplemented with 500 microM myristate. Studies in an immunosuppressed-mouse model of C. albicans infection revealed that the NMT/delta nmt strain produced 100% lethality within 7 d after intravenous administration while the isogenic nmt delta/nmtG447G strain produced no deaths even after 21 d. These observations establish that Nmt is essential for vegetative growth of C. albicans and suggest that inhibitors of this acyltransferase may be therapeutically useful fungicidal agents.
Near‐Infrared Spectroscopy of Polymers and Rubbers (2000)

Abstract Molecular spectroscopy as provided using the near‐infrared (NIR) measurement technique is valuable for polymer identification, characterization, and quantitation. NIR spectroscopy can be completed for in situ process applications where no sample preparation is required, and where rugged optical systems are a necessity. The NIR region is a complimentary band of the electromagnetic spectrum to the mid‐infrared (MIR) region (4000–500 cm −1 ), encompassing 13 333–4000 cm −1 or 750–2500 nm (nanometers, 10 −9 m). NIR and infrared (IR) spectroscopy are routinely used to qualify monomers prior to polymerization reactions. NIR is used to measure the kinetics of polymer onset and can be used to detect end‐point completion and initiator compound levels in polymerization reactions. NIR spectroscopy can also be used to sort polymers and to control the quality of incoming raw monomers and finished polymeric materials. Molecular spectroscopy using the NIR and IR measurement techniques is often used for competitive analysis and to determine thermal or photoinduced oxidation or degradation reactions in polymers. This article delineates the background, theory, band assignments, and applications of NIR spectroscopy for the measurement of polymers and rubbers.
Endogenous Neurogenesis Replaces Oligodendrocytes and Astrocytes after Primate Spinal Cord Injury (2006)

Neurogenesis has been described in various regions of the CNS throughout life. We examined the extent of natural cell division and replacement from 7 weeks to 7 months after cervical spinal cord injury in four adult rhesus monkeys. Bromodeoxyuridine (BrdU) injections revealed an increase of >80-fold in the number of newly divided cells in the primate spinal cord after injury, with an average of 725,000 BrdU-labeled cells identified per monkey in the immediate injury zone. By 7 months after injury, 15% of these new cells expressed mature markers of oligodendrocytes and 12% expressed mature astrocytic markers. Newly born oligodendrocytes were present in zones of injury-induced demyelination and appeared to ensheath or remyelinate host axons. Thus, cell replacement is an extensive natural compensatory response to injury in the primate spinal cord that contributes to neural repair and is a potential target for therapeutic enhancement.
Geocoding Natural Route Descriptions using Sidewalk Network Databases (2005)

People use descriptions referring to places through their daily life. These descriptions correspond to the region of the real world. We call such descriptions geo-referenced descriptions. We have studied a method of converting such descriptions like addresses and place names into their corresponding geographic coordinates, that is, tuples of longitude and latitude. The process of converting descriptions into coordinates is called geocoding. In this paper, we focus on natural route descriptions as a new type of target to geocode. We first propose Formal Route Statement (FRS) to represent and process natural route descriptions by means of a computer, and then explain a core schema of sidewalk network databases on the basis of a characteristic of natural route descriptions. Also, we present our prototype system to geocode natural route descriptions using sidewalk network databases based on our proposed framework.
Differential Scanning Calorimetric Study of the Thermal Unfolding Transitions of Yeast Iso-1 and Iso-2 Cytochromes c and Three Composite Isoenzymes (1994)

The effects of regional sequence differences on the thermodynamic stability of a globular protein have been investigated by scanning microcalorimetry. Thermal transitions have been measured for two isozymes of yeast cytochrome c (iso-1-MS and iso-2) and three composite proteins (Comp1-MS, Comp2-MS, and Comp3-MS) in which amino acid segments are exchanged between the parental isozymes. There are three main observations. (1) In the temperature range of the unfolding transitions (40-60 degrees C) the unfolding free energies for the composite proteins are only slightly different from those of the parental isozymes, although in some cases there are large but compensating changes in the transitional enthalpy and entropy. At lower temperatures (0-30 degrees C), all the composites are significantly less stable than the two parental proteins. (2) Long-range structural effects are responsible for at least some of the observed differences in stability. For example, in the temperature range of the unfolding transitions (40-60 degrees C), the Comp1-MS protein which contains only a small amount of iso-2-like sequence is less stable than either of the parental isozymes, despite the fact that none of the iso-2-specific amino acid side chains impinges directly on any of the iso-1-specific amino acid side chains. (3) Changes in ionization of His 26 appear to be linked to thermal unfolding. Iso-1-MS and Comp1-MS contain a histidine residue at position 26 while iso-2 and the other two composites do not. On lowering the pH from pH 6 to 5, both iso-1-MS and Comp1-MS show a decrease in stability (lower Tm) within the unfolding transition region (40-60 degrees C), whereas the stabilities of iso-2, Comp2-MS, and Comp3-MS are essentially unchanged. The thermal unfolding transitions are highly reversible (> 95%) but mechanistically complex. A moderate dependence of Tm on protein concentration and the ratio of the van't Hoff enthalpy to the calorimetric enthalpy suggest that thermal unfolding involves the reversible association of a significant fraction of the unfolded species, at least at elevated protein concentrations.
Spectroscopic Properties, Excitation, and Electron Transfer in an Anionic Water-Soluble Poly(fluorene-<i>alt</i>-phenylene)-perylenediimide Copolymer (2012)

An anionic fluorene-phenylene poly{1,4-phenylene-[9,9-bis(4-phenoxy-butylsulfonate)]fluorene-2,7-diyl}-based copolymer containing on-chain perylenediimine (PDI) chromophoric units, PBS-PFP-PDI, was synthesized and its photophysical properties studied as aggregates and isolated chains in water and dioxane/water (1:1) solution. UV-vis and emission spectroscopy measurements, time-correlated single photon counting, and wide field imaging have been employed to investigate the excited-state behavior of the PBS-PFP-PDI copolymer, including the effect of environment on the energy and electron transfer to the on-chain PDI chromophore. Although the Förster overlap integral is favorable, no evidence is found for intramolecular singlet excitation energy transfer in isolated copolymer chains in solution. Fluorescence is suggested to involve an interchain process, thus revealing that isolated copolymer chains in solution do not undergo efficient intramolecular energy transfer. However, quenching of the PBS-PFP excited state by PDI is observed in aqueous media and ultrafast pump-probe studies in water or dioxane-water solutions show that electron transfer occurs from the phenylene-fluorene units to the PDI. The extent of electron transfer increases with aggregation, suggesting it is largely an interchain process. The interaction of the negatively charged PBS-PFP-PDI copolymer with the positively charged surfactant hexadecyltrimethylammonium bromide (CTAB) in solution has also been studied. The copolymer PBS-PFP-PDI aggregates with the surfactant already at concentrations below the critical micelle concentration (cmc) and the nonpolar environment allows intermolecular energy transfer, observed by the weak emission band located at 630 nm that is associated with the emission of the PDI chromophore. However, the fact that the PDI photoluminescence (PL) lifetime (~1.4 ns) obtained in the presence of CTAB is considerably shorter than that of the nonaggregated chromophore (~5.4 ns) suggests that even in this case there is considerable PL quenching, possibly through some charge transfer route. The increase of the PBS-PFP-PDI photoluminescence intensity at surfactant concentrations above the cmc indicates deaggregation of polyelectrolyte within the initially formed polyelectrolyte-surfactant aggregates.
Well-balanced commensal microbiota contributes to anti-cancer response in a lung cancer mouse model (2015)

The intestinal microflora affects inflammation and immunity, not only locally at the mucosal level but also systemically, raising the question of whether the microflora affects inflammatory processes that contribute to cancer and its therapy. Prebiotics have also been found to play an antitumor role that is not limited to the gut. We investigated the antitumor roles of the intestinal microbiota using the Lewis lung cancer mouse model. In mice treated with cisplatin combined with ABX (an antibiotic cocktail of vancomycin, ampicillin, and neomycin), which can destroy the host commensal microflora, the tumor size was larger than in mice on a single treatment of cisplatin. Moreover, the survival rate of mice treated with cisplatin combined with ABX was significantly reduced. In contrast, mice treated with cisplatin combined with Lactobacillus bacteria had smaller tumors and an improved survival rate. Further study on gene expression indicated that ABX can partially impair the function of cisplatin by upregulating the expression of VEGFA and downregulating the expression of BAX and CDKN1B. The expression of IFN-γ, GZMB, and PRF1 in the CD8(+) T cells of these mice was reduced by ABX, indicating an immuno-enhancement role of commensal microbiota. Conversely, Lactobacillus co-treatment mice showed an enhanced antitumor response with upregulated IFN-γ, GZMB, and PRF1 expression. We conclude that the commensal microbiota contributes to the anti-lung cancer response and probiotics co-treatment can enhance the antigrowth and proapoptotic effects of cisplatin.
Effect of Some Phytogenic Agents and Synthetic Compounds on Complement Cascade-Mediated Hemolysis (1994)

A variety of anti-inflammatory compounds obtained from various medicinal plants (phytogenic) as well as some synthetic compounds were tested on the complement cascade in vitro. Bovine erythrocytes were treated with rabbit antibovine red blood cell antibody. Rabbit plasma was diluted with veronal buffer and mixed with erythrocytes in the presence or absence of drugs and incubated. Erythrocytes were pelleted and the absorbance of the supernatant at 412 nm determined. Drugs could be grouped into three categories; (a) those with no effect whatsoever; (b) those which produced definite enhancement of the release of hemoglobin by the complement cascade, and (c) prednisolone, which inhibited the release of hemoglobin by the complement cascade. We suggest that prednisolone and the drugs which had no effect on the complement cascade are safer to use as anti-inflammatory agents, while drugs enhancing the complement cascade may have potential adverse properties.