gebhart/patrepeval huggingface dataset:
Animal antimicrobial peptides: An overview (1998)

Antibiotic peptides are a key component of the innate immune systems of most multicellular organisms. Despite broad divergences in sequence and taxonomy, most antibiotic peptides share a common mechanism of action, i.e., membrane permeabilization of the pathogen. This review provides a general introduction to the subject, with emphasis on aspects such as structural types, post-translational modifications, mode of action or mechanisms of resistance. Some of these questions are treated in depth in other reviews in this issue. The review also discusses the role of antimicrobial peptides in nature, including several pathological conditions, as well as recent accounts of their application at the preclinical level.
Transition-metal phosphors with cyclometalating ligands: fundamentals and applications (2009)

One goal of this critical review is to provide advanced methodologies for systematic preparation of transition-metal based phosphors that show latent applications in the field of organic light emitting diodes (OLEDs). We are therefore reviewing various types of cyclometalating chelates for which the favorable metal-chelate bonding interaction, on the one hand, makes the resulting phosphorescent complexes highly emissive in both fluid and solid states at room temperature. On the other hand, fine adjustment of ligand-centered pi-pi* electronic transitions allows tuning of emission wavelength across the whole visible spectrum. The cyclometalating chelates are then classified according to types of cyclometalating groups, i.e. either aromatic C-H or azolic N-H fragment, and the adjacent donor fragment involved in the formation of metallacycles; the latter is an N-containing heterocycle, N-heterocyclic (NHC) carbene fragment or even diphenylphosphino group. These cyclometalating ligands are capable to react with heavy transition-metal elements, namely: Ru(II), Os(II), Ir(III) and Pt(II), to afford a variety of highly emissive phosphors, for which the photophysical properties as a function of chelate or metal characteristics are systematically discussed. Using Ir(III) complexes as examples, the C--N chelates possessing both C-H site and N-heterocyclic donor group are essential for obtaining phosphors with emission ranging from sky-blue to saturated red, while the N--N chelates such as 2-pyridyl-C-linked azolates are found useful for serving as true-blue chromophores due to their increased ligand-centered pi-pi* energy gap. Lastly, the remaining NHC carbene and benzyl phosphine chelates are highly desirable to serve as ancillary chelates in localizing the electronic transition between the metal and remaining lower energy chromophoric chelates. As for the potential opto-electronic applications, many of them exhibit remarkable performance data, which are convincing to pave a broad avenue for further development of all types of phosphorescent displays and illumination devices (94 references).
Biglycan regulates the expression and sarcolemmal localization of dystrobrevin, syntrophin, and nNOS (2006)

The dystrophin-associated protein complex (DAPC) provides a linkage between the cytoskeleton and the extracellular matrix (ECM) and is also a scaffold for a host of signaling molecules. The constituents of the DAPC must be targeted to the sarcolemma in order to properly function. Biglycan is an ECM molecule that associates with the DAPC. Here, we show that biglycan null mice exhibit a mild dystrophic phenotype and display a selective reduction in the localization of alpha-dystrobrevin-1 and -2, alpha- and beta1-syntrophin, and nNOS at the sarcolemma. Purified biglycan induces nNOS redistribution to the plasma membrane in cultured muscle cells. Biglycan protein injected into muscle becomes stably associated with the sarcolemma and ECM for at least 2 wk. This injected biglycan restores the sarcolemmal expression of alpha-dystrobrevin-1 and -2, and beta1- and beta2-syntrophin in biglycan null mice. We conclude that biglycan is important for the maintenance of muscle cell integrity and plays a direct role in regulating the expression and sarcolemmal localization of the intracellular signaling proteins dystrobrevin-1 and -2, alpha- and beta1-syntrophin and nNOS.
Neopeptide Antibiotics That Function as Opsonins and Membrane-Permeabilizing Agents for Gram-Negative Bacteria (2005)

We suggest a novel approach to enhancing antimicrobial drug action by utilizing engineered peptide conjugates. Our most potent conjugates, [fMLF]PMBN and [fMLF]PMEN, are nonapeptides derived from polymyxin B's (PMB's) cyclic moiety (Thr-Dab-cyclo[Dab-Dab-d-Phe-Leu-Dab-Dab-Thr], where Dab is 2,4-diaminobutyric acid) and polymyxin E's (PME's) cyclic moiety (Thr-Dab-cyclo[Dab-Dab-d-Leu-Leu-Dab-Dab-Thr]), respectively, attached to a linear tail comprised of formyl-Met-Leu-Phe (fMLF). The cyclic part binds to gram-negative lipopolysaccharides, rendering the bacterial outer membrane permeable to hydrophobic antibiotics. The tail confers chemotactic and opsonic activities upon the conjugates. These two activities appear to be the basis for the conjugates' antibacterial activities. The conjugates are 8 to 10 times less toxic than the parent PMB or PME antibiotics. Fourteen of 18 mice lethally challenged with erythromycin-resistant Klebsiella pneumoniae survived following intraperitoneal administration of erythromycin and [fMLF]PMBN, whereas erythromycin or the peptide conjugate alone had no effect. Moreover, the clearance of Klebsiella from blood was markedly enhanced by intravenous injection of the [fMLF]PMEN peptide conjugate compared to the clearance of the organism from the mice treated with buffer alone as a control and was similar to that achieved by the PME antibiotic. Blood clearance was also significantly enhanced by administration of PMEN either alone or in a mixture with fMLF, although the effect was less than that produced by the peptide conjugate. Since resistance to polymyxins, the parent molecules of the synthetic cyclic peptides, is rare, the emergence of bacteria resistant to the antimicrobial properties of the peptide conjugates may be precluded as well.
Computed tomography-based evaluation of aortic annulus, prosthesis size and impact on early residual aortic regurgitation after transcatheter aortic valve implantation (2012)

OBJECTIVES: Computed tomography (CT) is an increasingly utilized method for the evaluation of patient suitability for transcatheter aortic valve implantation (TAVI). The aim of this study was to analyse the role of CT in the choice of prosthesis and the prevention of residual aortic regurgitation (RAR).
IgE and IgG binding of peptides expressed from fragments of cDNA encoding the major house dust mite allergen Der p I (1991)

Large peptides expressed from cDNA fragments of a clone encoding the mite allergen Der p I were able to bind IgE and IgG in sera from allergic individuals. The binding was found for peptides from sequences throughout the molecule, with at least five regions, comprising residues 1-56, 53-99, 98-140, 166-194, and 188-222. The only limitation was that more than 30 amino acid residues were required for consistent binding. Each of seven sera examined showed a different profile of antibody binding to the peptides. For the most part the pattern of IgE and IgG binding to the peptides for each serum was similar, demonstrating a concordant repertoire. In 5/7 sera, however, IgG bound to some peptides which had little or no IgE binding activity, thus showing more diverse specificities. It is suggested that some divergence of repertoire can develop during the maturation of the B cell response.
When contemporary aminoacyl-tRNA synthetases invent their cognate amino acid metabolism (2003)

Faithful protein synthesis relies on a family of essential enzymes called aminoacyl-tRNA synthetases, assembled in a piecewise fashion. Analysis of the completed archaeal genomes reveals that all archaea that possess asparaginyl-tRNA synthetase (AsnRS) also display a second ORF encoding an AsnRS truncated from its anticodon binding-domain (AsnRS2). We show herein that Pyrococcus abyssi AsnRS2, in contrast to AsnRS, does not sustain asparaginyl-tRNAAsn synthesis but is instead capable of converting aspartic acid into asparagine. Functional analysis and complementation of an Escherichia coli asparagine auxotrophic strain show that AsnRS2 constitutes the archaeal homologue of the bacterial ammonia-dependent asparagine synthetase A (AS-A), therefore named archaeal asparagine synthetase A (AS-AR). Primary sequence- and 3D-based phylogeny shows that an archaeal AspRS ancestor originated AS-AR, which was subsequently transferred into bacteria by lateral gene transfer in which it underwent structural changes producing AS-A. This study provides evidence that a contemporary aminoacyl-tRNA synthetase can be recruited to sustain amino acid metabolism.
Low-Temperature UV-Processing of Nanocrystalline Nanoporous Thin TiO2 Films: An Original Route toward Plastic Electrochromic Systems (2008)

The direct UV irradiation of nanoparticulate TiO2 films deposited by the “doctor-blade” technique led to 1.1 μm thick nanoporous and nanocrystalline anatase layers on various kinds of substrates as evidenced by various characterization techniques (MET, SEM, XRD, TGA-MS, and N2 sorption measurements). These films demonstrated high electrochromic responses and coloration efficiencies in an ionic liquid containing a lithium salt, which is a stable and environmental friendly electrolyte. The coloration efficiency reached 38 cm2 C−1 for films on ITO/plastic, for a 0.65 absorption change at 710 nm, whereas the corresponding film on FTO/glass showed a 40 cm2 C−1 coloration efficiency for a 1.1 absorbance change at 710 nm. The high surface area, nanoporous texture, and nanoparticulate structure of these layers provide a large number of intercalation sites, and minimal diffusion path lengths are ensured by the high surface-to-volume ratio.
Expression of chemokine receptor CXCR4 in nasopharyngeal carcinoma: pattern of expression and correlation with clinical outcome (2005)

Nasopharyngeal carcinoma (NPC) is a tumor derived from epithelial cells and Epstein-Barr virus infection has been reported to be a cause of this disease. Chemokine receptor CXCR4 was found to be involved in HIV infection and was highly expressed in human malignant breast tumors and the ligand for CXCR4, CXCL12 (SDF-1), exhibited high expression in organs in which breast cancer metastases are often found. The metastatic pattern of NPC is quite similar to that of malignant breast tumors. In this study, we investigated the expression of CXCR4 in nasopharyngeal carcinoma (NPC) tissues by immunohistostaining. We found different staining patterns, which included localization in the nucleus, membrane, cytoplasm or a combination of them. The staining intensity was also variable among samples. The metastatic rates in patients with high compared to low or absent expression was 38.6% versus 19.8%, respectively (P = 0.004). High expression of CXCR4 was associated with poor overall survival (OS = 67.05% versus 82.08%, P = 0.0225). These results suggest that CXCR4 may be involved in the progression of NPC and that a high level of CXCR4 expression could be used as a prognostic factor.
Structurally and functionally conserved regions of cytochrome P-450 reductase as targets for DNA amplification by the polymerase chain reaction. Cloning and nucleotide sequence of the Schizosaccharomyces pombe cDNA (1992)

1. Alignments of the available cytochrome P-450 reductase amino acid sequences, and comparison with the crystal structure of ferredoxin-NADP reductase, indicate that two highly conserved regions are of functional importance. 2. Degenerate oligonucleotide primers, based on these sequences, were used in the polymerase chain reaction to amplify a 309 bp fragment of the cytochrome P-450 reductase gene from Schizosaccharomyces pombe for use as an homologous probe. 3. A 2.6 kb cDNA was cloned from a lambda library, and sequencing revealed an open-reading frame of 2034 bp encoding a protein of M(r) 76774. This protein shares 38-41% identity with other eukaryotic cytochrome P-450 reductases, and 30% identity with that of Bacillus megaterium. 4. Comparison of the N-terminal FMN-binding domain with flavodoxin, and the C-terminal FAD- and NADP-binding domain with ferredoxin-NADP reductase, indicates the presence of several functionally conserved regions. 5. The Sc. pombe cytochrome P-450 reductase gene was shown to contain no introns.
Direct binding of a soluble natural killer cell inhibitory receptor to a soluble human leukocyte antigen-Cw4 class I major histocompatibility complex molecule. (1996)

Natural killer (NK) cells expressing specific p58 NK receptors are inhibited from lysing target cells that express human leukocyte antigen (HLA)-C class I major histocompatibility complex molecules. To investigate the interaction between p58 NK receptors and HLA-Cw4, the extracellular domain of the p58 NK receptor specific for HLA-Cw4 was overexpressed in Escherichia coli and refolded from purified inclusion bodies. The refolded NK receptor is a monomer in solution. It interacts specifically with HLA-Cw4, blocking the binding of a p58-Ig fusion protein to HLA-Cw4-expressing cells, but does not block the binding of a p58-Ig fusion protein specific for HLA-Cw3 to HLA-Cw3-expressing cells. The bacterially expressed extracellular domain of HLA-Cw4 heavy chain and beta2-microglobulin were refolded in the presence of a HLA-Cw4-specific peptide. Direct binding between the soluble p58 NK receptor and the soluble HLA-Cw4-peptide complex was observed by native gel electrophoresis. Titration binding assays show that soluble monomeric receptor forms a 1:1 complex with HLA-Cw4, independent of the presence of Zn2+. The formation of complexes between soluble, recombinant molecules indicates that HLA-Cw4 is sufficient for specific ligation by the NK receptor and that neither glycoprotein requires carbohydrate for the interaction.
Implications of conceptualizations of the self for interview based research: Making meaning from interview data (2006)

Qualitative research is very often concerned with uncovering the basic structure or essence of whatever is being examined so that conclusions can be drawn and principles developed. Postmodernism with its focus on language and with people interacting with one another in the construction of their worlds provides a strong challenge to this. This has particular implications for a construct such as ‘self’. The post‐modern position is that ideas of the self are formed through social interaction in particular social contexts and are therefore not within the individual but within the space between people. This article explores the concept of ‘self’ as understood by recent writers and examines the implications for our understandings of the self gained through interview based research.
eXtended block cache (2002)

This paper describes a new instruction-supply mechanism, called the eXtended Block Cache (XBC). The goal of the XBC is to improve on the Trace Cache (TC) hit rate, while providing the same bandwidth. The improved hit rate is achieved by having the XBC a nearly redundant free structure. The basic unit recorded in the XBC is the extended block (XB), which is a multiple-entry single-exit instruction block. A XB is a sequence of instructions ending on a conditional or an indirect branch. Unconditional direct jumps do not end a XB. In order to enable multiple entry points per XB, the XB index is derived from the IP of its ending instruction. Instructions within the XB are recorded in reverse order, enabling easy extension of XBs. The multiple entry-points remove most of the redundancy. Since there is at most one conditional branch per XB, we can fetch up to n XBs per cycle by predicting n branches. The multiple fetch enables the XBC to march the TC bandwidth.
Epitope mapping and functional analysis of three murine IgG1 monoclonal antibodies to human tumor necrosis factor- alpha . (1993)

Immunologic and enzyme digest epitope mapping techniques were used to compare and contrast the interactions of three mouse mAb, designated A10G10, A6, and B6, with human TNF-alpha. These antibodies have previously been shown to protect mouse and human cells from TNF toxicity. ELISA showed that the antibodies recognize predominantly conformational epitopes, and that native TNF binds at least two molecules of the same mAb. Enzyme digestion of native TNF bound to each of the mAb in turn showed that each of the antibodies binds to or sterically masks a large fraction of the exposed surface of TNF. These epitope mapping data were compared with four putative TNF cell receptor binding sites presented in the literature. The results are consistent with the hypothesis that these antibodies prevent TNF-induced cell death by binding to or sterically masking the TNF receptor binding site.
A Single Vaccination with Polyomavirus VP1/VP2Her2 Virus-Like Particles Prevents Outgrowth of HER-2/neu–Expressing Tumors (2005)

Murine polyomavirus (MPyV) VP1 virus-like particles (VLPs), containing a fusion protein between MPyV VP2 and the extracellular and transmembrane domain of HER-2/neu (Her2), Her2(1-683)PyVLPs, were tested for their ability to vaccinate against Her2-expressing tumors in two different in vivo models. Protection was assessed both against a lethal challenge with a BALB/c mammary carcinoma transfected with human Her2 (D2F2/E2) and against the outgrowth of autochthonous mammary carcinomas in BALB-neuT mice, transgenic for the activated rat Her2 oncogene. A single injection of Her2(1-683)PyVLPs before tumor inoculation induced a complete rejection of D2F2/E2 tumor cells in BALB/c mice. Similarly, a single injection of Her2(1-683)PyVLPs at 6 weeks of age protected BALB-neuT mice with atypical hyperplasia from a later outgrowth of mammary carcinomas, whereas all controls developed palpable tumors in all mammary glands. VLPs containing only VP1 and VP2 did not induce protection. The protection elicited by Her2(1-683)PyVLPs vaccination was most likely due to a cellular immune response because a Her2-specific response was shown in an ELISPOT assay, whereas antibodies against Her2 were not detected in any of the two models. The results show the feasibility of using MPyV-VLPs carrying Her2 fusion proteins as safe and efficient vaccines against Her2-expressing tumors.
Identification of Endothelin Receptors by Chemical Cross-Linking (1990)

Specific binding sites for human/porcine endothelin have been found in rat brain membrane preparations using an [125I]endothelin. The apparent Kd value was 3 +/- 2 nM with a Bmax value of 2,200 +/- 200 fmol/mg protein. Chemical cross-linking of [125I]endothelin to rat brain membranes by using the cross-linking reagent disuccinimidyl suberate (DSS) revealed two specific proteins of Mr = 52,000 and Mr = 30,000. The same results were obtained by photoaffinity labeling of [125I]azidoendothelin to rat brain membranes. The labeling of the two proteins was inhibited in a dose-dependent manner by unlabeled endothelin but not by unrelated peptides. Peptide map comparisons of the Mr = 52,000 and Mr = 30,000 protein bands using Staphylococcus aureus V8 protease and papain revealed that the Mr = 30,000 band is a proteolytic degradation product of the Mr = 52,000. The apparent mol wt of the endothelin receptor is, therefore, 50,000, subtracting the mol wt of the iodinated endothelin.
The Stokes-Einstein law for diffusion in solution (1924)

Abstract Einstein has shown that the relation between molecular movement and diffusion in a liquid may be expressed by the following equation, when the particles move independently of each other:— D=͞Δ2/2t, (1) D being the diffusion constant and ͞Δ2 the mean square of the deviation in a given direction in time t. Further, if it be assumed that the particles possess the same mean kinetic energy as gas molecules at the same temperature, the following equation holds ͞Δ = 2RT/N . t/C (2) where R is the gas constant, N Avogadro’s number, T the absolute temperature, and C a constant, which we might call the frictional resistance of the molecule. Hence, D = RT/N .1/C. (3) Under the foregoing assumptions equations (2) and (3) hold equally well for dissolved molecules and particles of greater dimensions.
Hemodynamic Changes During Induction of Anesthesia with Eltanolone and Propofol in Dogs (1995)

The purpose of this study was to examine global and regional hemodynamic changes during induction of anesthesia with eltanolone, a new short-acting steroid hypnotic, as compared to propofol, in chronically instrumented dogs. The effects on cardiac performance were assessed in six animals. Renal and hepatic blood flows were examined in a separate study including five animals. Two doses of each drug were investigated: eltanolone 2.5 and 5 mg/kg and propofol 7.5 and 15 mg/kg. Left atrial filling pressures and cardiac output were not affected by either drug. Maximum rate of increase of left ventricular pressure decreased both with eltanolone (-28% and -40% from awake control for the 2.5 and 5 mg/kg doses, respectively) and with propofol (-19% and -30% from awake controls with 7.5 and 15 mg/kg, respectively). In contrast to propofol, eltanolone preserved arterial blood pressure. Propofol lowered systemic vascular resistance (-21% and -39% with the low and high dose, respectively), and only slightly decreased left ventricular wall thickening fraction (-16% and -21%). Eltanolone did not affect systemic vascular resistance but reduced the wall-thickening fraction dose-dependently (-28% and -61%). Propofol, but not eltanolone, induced moderate coronary vasodilation. Hepatic arterial blood flow velocity decreased dose-dependently (-21% and -64%) during eltanolone anesthesia whereas, in contrast, it increased after propofol (+59% and +64%). Renal and portal venous blood flows remained essentially unaltered from awake conditions. Our data demonstrate that both propofol and eltanolone have cardiodepressant properties but differ with regard to their effects on peripheral vascular tone. Systemic arterial vasodilation, as caused by propofol, may prove more favorable to overall cardiac performance. Liver blood flow was also better preserved with propofol when compared to eltanolone. (Anesth Analg 1995;81:125-31)
Generalization of the Dark Channel Prior for Single Image Restoration (2018)

Images degraded by light scattering and absorption, such as hazy, sandstorm, and underwater images, often suffer color distortion and low contrast because of light traveling through turbid media. In order to enhance and restore such images, we first estimate ambient light using the depth-dependent color change. Then, via calculating the difference between the observed intensity and the ambient light, which we call the scene ambient light differential, scene transmission can be estimated. Additionally, adaptive color correction is incorporated into the image formation model (IFM) for removing color casts while restoring contrast. Experimental results on various degraded images demonstrate the new method outperforms other IFM-based methods subjectively and objectively. Our approach can be interpreted as a generalization of the common dark channel prior (DCP) approach to image restoration, and our method reduces to several DCP variants for different special cases of ambient lighting and turbid medium conditions.
Intrahepatic T Cells in Hepatitis B (2000)

Clearance of the hepatitis B virus (HBV), a noncytopathic double-stranded DNA virus, requires the coordinated response of innate and adaptive, humoral and cellular immune systems. In more than 90% of immunocompetent adults who become infected, this immune response is quite vigorous, resulting in