gebhart/patrepeval huggingface dataset:
Interaction effects in topological superconducting wires supporting Majorana fermions (2011)

Among the broad spectrum of systems predicted to exhibit topological superconductivity and Majorana fermions, one-dimensional wires with strong spin-orbit coupling provide one of the most promising experimental candidates. Here we investigate the fate of the topological superconducting phase in such wires when repulsive interactions are present. Using a combination of density matrix renormalization group, bosonization, and Hartree--Fock techniques, we demonstrate that while interactions degrade the bulk gap---consistent with recent results of Gangadharaiah et al.---they also greatly expand the parameter range over which the topological phase arises. In particular, we show that with interactions this phase can be accessed over a broader chemical potential window, thereby leading to greater immunity against disorder-induced chemical potential fluctuations in the wire. We also suggest that in certain wires strong interactions may allow Majorana fermions to be generated without requiring a magnetic field.
The lability of behavior as a marker of comorbid depression and anxiety (2010)

This study examines nine dynamical and three emotional aspects of behavior in depression and anxiety, singly and comorbidly. The study employs the Structure of Temperament Questionnaire Compact (STQ 77), whose 12 scales assess the energetic, lability and sensitivity aspects of behavior in the physical, social, mental and emotional domains. The STQ 77 was administered to 86 patients with Major Depression, 85 patients with an anxiety disorder, 43 patients with comorbid depression and anxiety, and 71 subjects without depression or anxiety disorder all presenting to a private outpatient clinical practice. Results: 1) Depression was associated with self-reports of increased impulsivity and rigidity of behavior; 2) Depressed patients reported significantly lower physical energy, tempo of physical activity and plasticity of behavior. The presence of comorbid anxiety further worsened these effects; 3) The ability to sustain attention on a mental task and to learn new information was lower in depressed patients than in other groups. Conclusions: comorbid depression and anxiety might be associates, decreasing adaptivity and the self-regulatory balance of behavior, leading to the de- velopment of extremes in behavioral reactivity (impulsivity and rigidity).v
Generic surface modification strategy for sensing applications based on Au/SiO2 nanostructures (2007)

A generic protocol for the creation of material-mediated self-assembled patterns of streptavidin, defined solely by patterns of gold and SiO(2), is presented. Protein-adsorption resistance of selected regions was obtained by material-specific adsorption of thiol-modified poly(ethylene)glycol (thiol-PEG) on gold followed by adsorption of poly-L-lysine (PLL) modified PEG (PLL-g-PEG) on SiO(2). Selective streptavidin binding to either gold or SiO(2) (or both) was ensured by introducing biotin-modified thiolated (thiol-biotin) and/or biotin-modified PLL-g-PEG (PLL-g-PEGbiotin) compounds. The introduction of biotin did not influence the protein-adsorption resistance. On the macroscopic scale, the protein-adsorption-resistant properties and the streptavidin-binding capacity were optimized using quartz crystal microbalance with dissipation monitoring. The reproduction of micrometer-scale gold patterns on SiO(2) into patterns of streptavidin was verified using fluorescence microscopy, while the compatibility of the material-specific surface-modification strategy with nanoscale features was accomplished by modifying a localized surface plasmon resonance (LSPR) active template, defined by randomly distributed nanoapertures in a thin gold film on SiO(2). The demonstrated compatibility of the latter substrate with LSPR-based label-free sensing of biorecognition reactions, combined with the fact that all compounds utilized are commercially available, makes the surface-modification protocol attractive as a generic surface modification solution for a broad range of biorecognition-based assays.
Zukunftsthemen des Controllings (2012)

Die Controlling - Zeitschrift für erfolgsorientierte Unternehmenssteuerung liefert Monat für Monat fundierte und anwendungsorientierte Fachbeiträge für das Management sowie das Finanz- und Rechnungswesen in Unternehmen. Klar gegliedert und strukturiert werden für alle Controlling-Bereiche die Faktoren für eine erfolgreiche Unternehmenssteuerung aufgezeigt.
Two-Photon Laser Scanning Fluorescence Microscopy (1990)

Molecular excitation by the simultaneous absorption of two photons provides intrinsic three-dimensional resolution in laser scanning fluorescence microscopy. The excitation of fluorophores having single-photon absorption in the ultraviolet with a stream of strongly focused subpicosecond pulses of red laser light has made possible fluorescence images of living cells and other microscopic objects. The fluorescence emission increased quadratically with the excitation intensity so that fluorescence and photo-bleaching were confined to the vicinity of the focal plane as expected for cooperative two-photon excitation. This technique also provides unprecedented capabilities for three-dimensional, spatially resolved photochemistry, particularly photolytic release of caged effector molecules.
In vitro selection of a 7-methyl-guanosine binding RNA that inhibits translation of capped mRNA molecules (1997)

Using systematic evolution of ligands by exponential enrichment (SELEX), an RNA molecule was isolated that displays a 1,000-fold higher affinity for guanosine residues that carry an N-7 methyl group than for nonmethylated guanosine residues. The methylated guanosine residue closely resembles the 5' terminal cap structure present on all eukaryotic mRNA molecules. The cap-binding RNA specifically inhibited the translation of capped but not uncapped mRNA molecules in cell-free lysates prepared from either human HeLa cells or from Saccharomyces cerevisiae. These findings indicate that the cap-binding RNA will also be useful in studies of other cap-dependent processes such as pre-mRNA splicing and nucleocytoplasmic mRNA transport.
Suzuki-Miyaura Cross-Coupling in Acylation Reactions, Scope and Recent Developments (2013)

Since the first report and due to its handiness and wide scope, the Suzuki-Miyaura (SM) cross coupling reaction has become a routine methodology in many laboratories worldwide. With respect to other common transition metal catalyzed cross couplings, the SM reaction has been so far less exploited as a tool to introduce an acyl function into a specific substrate. In this review, the various approaches found in the literature will be considered, starting from the direct SM acylative coupling to the recent developments of cross coupling between boronates and acyl chlorides or anhydrides. Special attention will be dedicated to the use of masked acyl boronates, alkoxy styryl and alkoxy dienyl boronates as coupling partners. A final section will be then focused on the acyl SM reaction as key synthetic step in the framework of natural products synthesis.
Analyses of Genotypic Diversity among North, South, and Central American Isolates ofSugarcane Yellow Leaf Virus: Evidence for Colombian Origins and for Intraspecific Spatial Phylogenetic Variation (2002)

ABSTRACT We have analyzed the genotypic diversity of Sugarcane yellow leaf virus (SCYLV) collected from North, South, and Central America by fingerprinting assays and selective cDNA cloning and sequencing. One group of isolates from Colombia, designated the C-population, has been identified as residing at the root node between a separable superpopulation structure of SCYLV and other members of the family Luteoviridae , indicating that the progenitor viruses of the North, South, and Central American isolates of the SCYLV superpopulation most likely arose from a C-population structure. From a model of intrafamilial evolution (F. Moonan et al., Virology 269:156–171, 2000), a prediction could be made that within the SCYLV species, the capacity of genomic sequence divergence would range from lowest in the capsid protein open reading frame 3 (ORF 3) to highest in a region spanning across the carboxy-terminal end of the RNA-dependent RNA polymerase ORF. We have demonstrated the validity and applicability of this intrafamilial model for the prediction of intraspecies SCYLV diversity. Analysis of spatial phylogenetic variation (SPV) within the SCYLV isolates could not be assessed by application of a “partial likelihoods assessed through optimization” (PLATO)-derived intraspecies model alone. However, application of a PLATO-derived intrafamilial model with the intraspecies-derived model allowed distinction of three forms of SPV. Two of the SPV forms identified correspond to the extremes in a continuum of sequence evolution displayed in a SCYLV superpopulation structure, and the third form was diagnostic of a C-population structure. The application of these types of models has value in terms of predicting the types of SCYLV intraspecies diversity that may exist worldwide, and in general, may be useful in application for more informed design of transgenes for use in the elicitation of homology-dependent virus resistance mechanisms in transgenic plants.
FGF signaling inhibits chondrocyte proliferation and regulates bone development through the STAT-1 pathway (1999)

Several genetic forms of human dwarfism have been linked to activating mutations in FGF receptor 3, indicating that FGF signaling has a critical role in chondrocyte maturation and skeletal development. However, the mechanisms through which FGFs affect chondrocyte proliferation and differentiation remain poorly understood. We show here that activation of FGF signaling inhibits chondrocyte proliferation both in a rat chondrosarcoma (RCS) cell line and in primary murine chondrocytes. FGF treatment of RCS cells induces phosphorylation of STAT-1, its translocation to the nucleus, and an increase in the expression of the cell-cycle inhibitor p21WAF1/CIP1. We have used primary chondrocytes from STAT-1 knock-out mice to provide genetic evidence that STAT-1 function is required for the FGF mediated growth inhibition. Furthermore, FGF treatment of metatarsal rudiments from wild-type and STAT-1(-/-) murine embryos produces a drastic impairment of chondrocyte proliferation and bone development in wild-type, but not in STAT-1(-/-) rudiments. We propose that STAT-1 mediated down regulation of chondrocyte proliferation by FGF signaling is an homeostatic mechanism which ensures harmonious bone development and morphogenesis.
A versatile, efficient strategy for assembly of multi-fragment expression vectors in Saccharomyces cerevisiae using 60 bp synthetic recombination sequences (2013)

The presented method delivers a substantial improvement for assembly of multi-fragment expression vectors in S. cerevisiae. Not only does it improve the efficiency of in vivo assembly, but it also offers a versatile platform for easy and rapid design and assembly of synthetic constructs. The presented method is therefore ideally suited for the construction of complex pathways and for high throughput strain construction programs for metabolic engineering purposes. In addition its robustness and ease of use facilitate the construction of any plasmid carrying two or more genes.
Lethal neonatal Hutchinson‐Gilford progeria syndrome (1999)

We report on a 35-week gestation female fetus with Hutchinson-Gilford progeria (HGP). This patient, who is the first reported with neonatal HGP in the English literature but is the fourth, counting three previous French cases, supports the existence of a more severe prenatal form of progeria. She died 7 hours after birth and presented with intrauterine growth retardation, premature aging, absence of subcutaneous fat, brachydactyly, absent nipples, hypoplastic external genitalia, and abnormal ear lobes. The child's combination of clinical and skeletal manifestations differentiates this form of HGP from other progeroid syndromes with neonatal presentation. We also report previously undescribed autopsy findings including premature loss of hair follicles, premature regression of the renal nephrogenic layer, and premature closure of the growth plates in the distal phalanges that may be related to the aging processes in this condition. We could not find any histological data to support acro-osteolysis, which is the radiographic sign of brachydactyly. The terminal phalanges in HGP seem to be underdeveloped rather than osteolytic. Am. J. Med. Genet. 82:242–248, 1999. © 1999 Wiley-Liss, Inc.
The membrane current of single rod outer segments. (1979)

1. Outer segments of individual rods in the retina of the toad, Bufo marinus, were drawn into a glass pipette to record the membrane current. 2. Light flashes evoked transient outward currents. The peak response amplitude was related to flash intensity by a Michaelis equation with half-saturating intensity about 1 photon mum-2. 3. The saturating response amplitude ranged up to 27 pA and corresponded closely to complete suppression of the steady inward current present in darkness. 4. For a given cell the saturating response amplitude varied linearly with the length of outer segment within the pipette. This is consistent with a uniform density of light-sensitive channels and negligible gradient of membrane potential along the outer segment. 5. Responses to bright flashes never showed the relaxation from an initial peak seen previously in intracellular voltage recordings, suggesting that the conductance change responsible for the relaxation does not occur in the outer segment. 6. Responses to local illumination of only the recorded outer segment were very similar to those obtained with diffuse light at the same intensity, indicating that peripheral rods made little contribution to the responses. 7. The spectral sensitivity of 'red' rods was consistent with a retinal1-based pigment with lambda max = 498 +/- 2 nm. 8. The kinetics of the response were consistent with four stages of delay affecting action of the internal transmitter. Responses were faster at the basal end of the outer segment than at the distal tip. 9. Background light reduced the sensitivity to a superposed dim test flash and shortened the time course of the response, indicating that adapting light modifies the kinetics and gain of the transduction mechanism within the outer segment. 10. Responses to dim lights exhibited pronounced fluctuations which are attributed in the succeeding paper (Baylor, Lamb & Yau, 1979) to the quantal nature of light.
Nitrogen doped graphene nanoplatelets as catalyst support for oxygen reduction reaction in proton exchange membrane fuel cell (2010)

Graphene nanoplatelets have been synthesized by thermal exfoliation of graphitic oxide and nitrogen doped graphene nanoplatelets have been obtained by nitrogen plasma treatment. Graphene nanoplatelets and nitrogen doped graphene nanoplatelets have been used as a catalyst support for platinum nanoparticles for oxygen reduction reactions in proton exchange membrane fuel cells. Platinum nanoparticles were dispersed over these support materials using the conventional chemical reduction technique. The morphology and structure of the graphene based powder samples were studied using X-ray diffraction, Raman spectroscopy, transmission electron microscopy and X-ray photoelectron spectroscopy. A full cell was constructed with platinum loaded nitrogen doped graphene nanoplatelets and the results have been compared with platinum loaded graphene nanoplatelets. A maximum power density of 440 and 390 mW cm−2 has been obtained with platinum loaded nitrogen doped graphene and platinum loaded graphene nanoplatelets as ORR catalysts respectively. Nitrogen plasma treatment created pyrrolic nitrogen defects, which act as good anchoring sites for the deposition of platinum nanoparticles. The improved performance of fuel cells with N-G as catalyst supports can be attributed to the increased electrical conductivity and improved carbon–catalyst binding.
Phase-noise characteristics of a 25-GHz-spaced optical frequency comb based on a phase- and intensity-modulated laser (2013)

We investigated phase-noise characteristics of both a phase/intensity-modulated laser with 25-GHz mode spacing and a mode-locked fiber laser with carrier-envelope-offset (CEO) locking. As the separation from the frequency of the continuous wave (CW) laser diode (LD) for a seed light source increases, the integrated phase noise of each comb mode of both the phase/intensity-modulated laser and supercontinuum light originating from it increases with the same slope as a function of mode number. The dependence of the integrated phase noise on mode number with the phase/intensity-modulated laser is much larger than with the mode-locked fiber laser of the CEO locking. However, the phase noise of the phase/intensity-modulated laser is extremely lower than that of the mode-locked fiber laser with CEO locking in the frequency region around the CW LD. The phase noise of the phase/intensity-modulated laser with 25-GHz mode spacing and that of the mode-locked fiber laser with the CEO locking could be estimated and were found to be almost the same at the wavelengths required in an f-to-2f self-referencing interferometer. Our experimental results indicate the possibility of achieving an offset-frequency-locked frequency comb with the phase/intensity-modulated laser.
The A9 antigen associated with aggressive human squamous carcinoma is structurally and functionally similar to the newly defined integrin alpha 6 beta 4. (1991)

We previously reported that altered expression of the A9 antigen (defined by monoclonal antibody UM-A9) is a predictive marker of early recurrence and progression of squamous cell carcinoma (SCC). In normal squamous cells A9 expression is limited to the site of contact with the basement membrane in vivo and the culture surface in vitro, whereas aggressive SCCs exhibit loss of polarity and increased intensity of A9 expression. The potential relationship of the A9 antigen to structures known to be involved in cell adhesion was analyzed by immunobiochemical and cell adhesion assays. UM-A9 precipitates a complex of protein chains reminiscent of the alpha and beta heterodimer glycoproteins that characterize the integrin family of extracellular matrix receptors. Proteins were isolated from A9-positive cells using UM-A9 and well-defined antibodies specific for integrin alpha and beta chains. UM-A9, anti-alpha 6, and anti-beta 4 monoclonal antibodies (mAbs) all precipitated proteins with comparable electrophoretic mobilities. Furthermore, UM-A9 mAb precleared the SCC alpha 6 beta 4 integrin complex isolated with anti-alpha 6 or anti-beta 4 mAbs but not that isolated by anti-beta 1 mAb. The isoelectric points of the A9 complex chains were consistent with those reported for alpha 6 and beta 4. Three of the polypeptide chains (140, 175, and 205 kDa) precipitated by UM-A9 showed peptide homology to one another and to the beta 4 chain precipitated by mAb 439-9B. The A9/alpha 6 subunit is composed of 125- and 30-kDa chains and was distinguished from beta 4 and beta 1 chains by its peptide map and isoelectric point. UM-A9 binds to an epitope common to the beta 4 subunits since in pulse-chase analysis the beta 4 species are precipitated at an early time point, whereas detection of alpha-subunit synthesis is detected during assembly of the mature complex. Immunoprecipitation and preclearing experiments demonstrated that in SCC the alpha 6 subunit is associated primarily with the beta 4 species and not with the 130-kDa beta 1 subunit. In cell adhesion assays on extracellular matrix proteins, the alpha 6-specific GoH3 mAb inhibited binding of SCC to laminin, suggesting that alpha 6 beta 4 may function as a laminin receptor in SCC. These data and our prior observations showing an association between altered A9 expression and early recurrence in SCC provide the first evidence that altered expression of alpha 6 beta 4 integrin is associated with the clinical behavior of human squamous cell carcinomas.
GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized libraries (2008)

There are many methods for introducing random mutations into nucleic acid sequences. Previously, we described a suite of programmes for estimating the completeness and diversity of randomized DNA libraries generated by a number of these protocols. Our programmes suggested some empirical guidelines for library design; however, no information was provided regarding library diversity at the protein (rather than DNA) level. We have now updated our web server, enabling analysis of translated libraries constructed by site-saturation mutagenesis and error-prone PCR (epPCR). We introduce GLUE-Including Translation (GLUE-IT), which finds the expected amino acid completeness of libraries in which up to six codons have been independently varied (according to any user-specified randomization scheme). We provide two tools for assisting with experimental design: CodonCalculator, for assessing amino acids corresponding to given randomized codons; and AA-Calculator, for finding degenerate codons that encode user-specified sets of amino acids. We also present PEDEL-AA, which calculates amino acid statistics for libraries generated by epPCR. Input includes the parent sequence, overall mutation rate, library size, indel rates and a nucleotide mutation matrix. Output includes amino acid completeness and diversity statistics, and the number and length distribution of sequences truncated by premature termination codons. The web interfaces are available at http://guinevere.otago.ac.nz/stats.html.
Involvement and identification of a tryptophanyl residue at the pyruvate binding site of transcarboxylase (1988)

Transcarboxylase (TC) from Propionibacterium shermanii consists of a central hexameric 12S subunit to which 6 outer dimeric 5S subunits are attached through 12 biotinyl 1.3S subunits. The enzyme catalyzes the transfer of a carboxyl group from methylmalonyl-CoA to pyruvate, forming oxalacetate and propionyl-CoA. The pyruvate binding site, located on the 5S subunit, was examined by monitoring the intrinsic fluorescence quenching accompanying the incremental addition of pyruvate to either TC or the 5S subunit. The quenching studies indicate that there are two binding sites for pyruvate with apparent dissociation constants of 0.23 and 1.25 mM for intact TC and of 0.18 and 1.20 mM for the outer 5S subunit. The microenvironment of the Trp(s) sensitive to pyruvate binding was analyzed by using the neutral quencher acrylamide. With TC, the fractional accessible fluorescence (fa) was 0.64, whereas a fa value of 0.56 was obtained in the presence of pyruvate. A 27% decrease in fa was observed with the outer 5S subunit in the presence of pyruvate as compared to the free 5S subunit. By labeling the outer subunit in the absence of pyruvate with 2,4-dinitrophenylsulfenyl chloride (DNPS-Cl), a tryptic peptide containing DNPS-labeled Trp was isolated; the sequence was determined and identified with the amino-terminal residues 67-75 of the outer subunit that has been derived from DNA-sequencing studies. Trp-73 contained the DNPS label; its labeling was inhibited by pyruvate. A sequence comparison with other biotinyl enzymes shows that the sequence 67-75 is highly conserved.(ABSTRACT TRUNCATED AT 250 WORDS)