gebhart/patrepeval huggingface dataset:
Pour some sugar on it: the expanding world of bacterial protein O‐linked glycosylation (2013)

Protein glycosylation was once considered as an eccentricity of a few bacteria. However in the recent years multiple O-glycosylation mechanisms have been identified in bacterial species from the most diverse genera, including various important human pathogens. This review focuses on summarizing the structural diversity, the various pathways and the physiological roles of this post-translational protein modification. We propose a classification of O-glycosylation based on the requirement of an oligosaccharyltransferase (OTase). OTase-dependent glycosylation utilizes an oligosaccharide synthesized on a lipid carrier that is transferred to proteins en bloc by an OTase. Multiple proteins, including the pilins, are glycosylated using this mechanism. OTase-independent glycosylation refers to the pathway in which glycosyltransferases sequentially add monosaccharides onto the target proteins. This pathway is employed for glycosylation of flagella and autotransporters. Both systems play key roles in pathogenesis. Exploiting glycosylation machineries it is now possible to generate glycoconjugates made of different proteins attached to polysaccharides derived from LPS or capsule biosynthesis. These recombinant glycoproteins can be exploited for vaccines and diagnostics of bacterial infections. Furthermore, O-glycosylation systems are promising targets for antibiotic development. Technological advances in MS and NMR will facilitate the discovery of novel glycosylation systems. Likely, the O-glycosylation pathways we currently know constitute just the tip of the iceberg of a still largely uncharacterized bacterial glycosylation world.
Twist overexpression promoted epithelial-to-mesenchymal transition of human peritoneal mesothelial cells under high glucose (2012)

In conclusion, HG-induced Twist expression might contribute to EMT of HPMCs. Twist may control EMT of HPMCs by regulating MMP9.
Purification and characterization of a bovine acetyl low density lipoprotein receptor. (1988)

The acetyl low density lipoprotein (LDL) receptor is expressed on macrophages and some endothelial cells and mediates macrophage-foam cell formation in culture. A 220-kDa acetyl LDL binding protein was partially purified from bovine liver membranes and was used to make a specific monoclonal antibody. The 220-kDa protein immunoprecipitated by this antibody retained binding activity, and the antibody was used to detect this protein in cells lining bovine liver sinusoids and on the surface of cultured bovine alveolar macrophages. In the human monocytic cell line THP-1, the expression of both acetyl LDL receptor activity and a 220-kDa acetyl LDL binding protein were dramatically induced in parallel after differentiation to a macrophage-like state induced by phorbol ester. The ligand specificity, tissue and cell-type specificity, and coinduction data indicated that this 220-kDa cell-surface binding protein is probably a receptor that mediates acetyl LDL endocytosis. The 220-kDa protein, which was purified 238,000-fold from bovine lung membranes to near homogeneity using monoclonal antibody affinity chromatography, is a trimer of 77-kDa subunits that contain asparagine-linked carbohydrate chains.
Mouse interleukin-1 receptor antagonist induced by Actinobacillus actinomycetemcomitans lipopolysaccharide blocks the effects of interleukin-1 on bone resorption and osteoclast-like cell formation (1994)

We have reported that P388D1 cell line murine macrophages stimulated with lipopolysaccharide (LPS) from Actinobacillus actinomycetemcomitans release interleukin-1 (IL-1) inhibitor. The IL-1 inhibitor was purified from conditioned media of P388D1 cells stimulated with A. actinomycetemcomitans LPS for 72 h to homogeneity by a four-step procedure: acetic acid extraction from conditioned media; Bio-Gel P-60 gel filtration chromatography; DEAE-Sepharose CL-6B column chromatography; and reverse-phase high-performance liquid chromatography on a C18 hydrophobic support. The purified IL-1 inhibitor gave a single band of protein with a molecular mass of 26 kDa on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The purified IL-1 inhibitor was a heat- and acid-stable protein that was inactivated by digestion with trypsin and reduction with dithiothreitol. This inhibitory factor suppressed the proliferation of C3H/HeJ mouse thymocytes and the proliferation of IL-1-dependent cell lines, D10.G4.1 and RPMI 1788, induced by IL-1. However, this inhibitor did not affect the proliferation of IL-2-dependent CTLL-2 cells induced by IL-2, the proliferation of C3H/HeJ mouse thymocytes stimulated with a mitogenic dose of concanavalin A, and the proliferation of IL-6-dependent B9 cells induced by IL-6. Furthermore, the IL-1 inhibitor significantly blocked stimulation of bone resorption in organ cultures of newborn mouse calvaria and inhibited the osteoclast-like cell formation in mouse marrow cultures. A monoclonal antibody prepared against the purified IL-1 inhibitor reacted with mouse recombinant IL-1 receptor antagonist (rIL-1ra), and a polyclonal antibody to mouse rIL-1ra reacted with the IL-1 inhibitor by Western blot (immunoblot) analysis. These results indicate that the IL-1 inhibitor is an identical molecule to rIL-1ra, suggesting that the IL-1 inhibitor (IL-1ra) released by macrophages stimulated with LPS from A. actinomycetemcomitans may play an important mediative role in the development of periodontal disease.
Cortical white-matter microstructure in schizophrenia (2007)

Our findings confirm the presence of cortical white-matter microstructure disruption in frontal and temporo-occipital lobes in the largest sample of people with schizophrenia thus for studied with this technique. Future brain imaging studies, together with genetic investigations, should further explore white-matter integrity and genes encoding myelin-related protein expression in people with first-episode schizophrenia and those at high risk of developing the disorder.
Native Protein Fluctuations: The Conformational-Motion Temperature and the Inverse Correlation of Protein Flexibility with Protein Stability (1998)

We study the fluctuations of native proteins by exact enumeration using the HP lattice model. The model fluctuations increase with temperature. We observe a low-temperature point, below which large fluctuations are frozen out. This prediction is consistent with the observation by Tilton et al. [R. F. Tilton, Jr., J. C. Dewan, and G. A. Petsko, Biochemistry 31, 2469 (1992)], that the thermal motions of ribonuclease A increase sharply above about 200 K. We also explore protein "flexibility" as defined by Debye-Waller-like factors and solvent accessibilities of core residues to hydrogen exchange. We find that proteins having greater stability tend to have fewer large fluctuations, and hence lower flexibilities. If flexibility is necessary for enzyme catalysis, this could explain why proteins from thermophilic organisms, which are exceptionally stable, may be catalytically inactive at normal temperatures.
Two phases of palmitate-induced insulin resistance in skeletal muscle: impaired GLUT4 translocation is followed by a reduced GLUT4 intrinsic activity (2007)

We examined, in soleus muscle, the effects of prolonged palmitate exposure (0, 6, 12, 18 h) on insulin-stimulated glucose transport, intramuscular lipid accumulation and oxidation, activation of selected insulin-signaling proteins, and the insulin-stimulated translocation of GLUT4. Insulin-stimulated glucose transport was progressively reduced after 6 h (-33%), 12 h (-66%), and 18 h (-89%) of palmitate exposure. These decrements were closely associated with concurrent reductions in palmitate oxidation at 6 h (-40%), 12 h (-60%), and 18 h (-67%). In contrast, intramuscular ceramide (+24%) and diacylglycerol (+32%) concentrations, insulin-stimulated AS160 (-36%) and PRAS40 (-33%) phosphorylations, and Akt (-40%), PKCtheta (-50%), and GLUT4 translocation (-40%) to the plasma membrane were all maximally altered within the first 6 h of palmitate treatment. No further changes were observed in any of these parameters after 12 and 18 h of palmitate exposure. Thus, the intrinsic activity of GLUT4 was markedly reduced after 12 and 18 h of palmitate treatment. During this reduced GLUT4 intrinsic activity phase at 12 and 18 h, the reduction in glucose transport was twofold greater compared with the early phase (< or =6 h), when only GLUT4 translocation was impaired. Our study indicates that palmitate-induced insulin resistance is provoked by two distinct mechanisms: 1) an early phase (< or =6 h), during which lipid-mediated impairments in insulin signaling and GLUT4 translocation reduce insulin-stimulated glucose transport, followed by 2) a later phase (12 and 18 h), during which the intrinsic activity of GLUT4 is markedly reduced independently of any further alterations in intramuscular lipid accumulation, insulin signaling and GLUT4 translocation.
Adenosine-receptor subtypes: their relevance to adenosine-mediated responses in asthma and chronic obstructive pulmonary disease (2002)

Adenosine administration by inhalation elicits concentration-related bronchoconstriction in subjects with asthma and chronic obstructive pulmonary disease (COPD). The mechanisms of adenosine-induced bronchoconstriction appear to involve a selective interaction with activated mast cells with subsequent release of preformed and newly-formed mediators. Further evidence linking adenosine signalling to asthma and COPD comes from the finding that many cell types that play important roles in the exacerbation of these conditions express adenosine receptors and demonstrate relevant effects through stimulation of these receptors. Therefore, blockade of these receptors may be a valuable approach to the treatment of asthma and chronic obstructive pulmonary disease. Promising adenosine-receptor targets for novel therapeutics of asthma and chronic obstructive pulmonary disease have recently been identified in a number of inflammatory cell types, including mast cells, eosinophils, lymphocytes, neutrophils, and macrophages. The recent characterisation of the A2B receptors indicates the human lung mast cell as one of the most strategic cellular targets.
Design of reflective relay for soft x-ray lithography (1991)

An all-reflective unobscured flat-field low-distortion telecentric optical design has been developed for non-scanning reduction soft x-ray lithography application. 1. 0
Ringing Ears: The Neuroscience of Tinnitus: Figure 1. (2010)

Tinnitus is a phantom sound (ringing of the ears) that affects quality of life for millions around the world and is associated in most cases with hearing impairment. This symposium will consider evidence that deafferentation of tonotopically organized central auditory structures leads to increased neuron spontaneous firing rates and neural synchrony in the hearing loss region. This region covers the frequency spectrum of tinnitus sounds, which are optimally suppressed following exposure to band-limited noise covering the same frequencies. Cross-modal compensations in subcortical structures may contribute to tinnitus and its modulation by jaw-clenching and eye movements. Yet many older individuals with impaired hearing do not have tinnitus, possibly because age-related changes in inhibitory circuits are better preserved. A brain network involving limbic and other nonauditory regions is active in tinnitus and may be driven when spectrotemporal information conveyed by the damaged ear does not match that predicted by central auditory processing.
Site‐specific cleavage reaction catalyzed by leadzyme is enhanced by combined effect of lead and rare earth ions (1996)

Lead-dependent ribozyme (leadzyme) is a ribozyme working with Pb2+. In this paper, we have investigated the combined effect of metal ions, especially rare earth ions, on the cleavage reaction by the leadzyme. As a result, it was observed that although only a rare earth ion or another divalent ion except Pb2+ did not play a role as the catalyst, the addition of a rare earth ion in the presence of Pb2+ increased significantly the yield of the cleavage reaction. The result suggests that the complex between the leadzyme and the substrate should have two classes of metal ion binding sites.
Molecular design of dopant precursors for atomic layer epitaxy of SrS:Ce (1999)

Two cerium compounds, Ce{N[Si(CH 3 ) 3 ] 2 } 3 and Ce(tmhd) 4 (tmhd=2,2,6,6-tetramethylheptane-3,5-dionate), have been evaluated for utilization in the preparation of thin films of SrS:Ce by atomic layer epitaxy (ALE). The resultant coatings have been characterized for use in electroluminescent (EL) devices. The observed emission maximum at 518 nm for the devices derived from Ce(tmhd) 4 shifts to 480 nm for those resulting from Ce{N[Si(CH 3 ) 3 ] 2 } 3 . This shift may be correlated with the basicity of the ligand present on the dopant element.
Efficient Rejection of Fluorescence from Raman Spectra Using Picosecond Kerr Gating (1999)

An efficient method for the rejection of fluorescence from picosecond time-resolved resonance Raman (ps-TR 3 ) spectra, applicable also to ground-state Raman spectroscopy, has been demonstrated. The technique removes fluorescence from Raman light in the time domain using a Kerr gate driven by 110 μJ, 1 ps pulses at 800 nm and a repetition rate of 0.65 kHz, giving a response time of ∼ 3 ps, representing the highest time resolution achieved experimentally for rejecting fluorescence from Raman spectra. The effectiveness of the method is proven by measuring Raman solvent bands and ps-TR 3 spectra of S 1 p-quaterphenyl from solutions contaminated with the laser dye DCM using laser wavelengths which excite the dye and so produce intense fluorescence emission. The optical transmittances accounting for losses in the optical elements and losses due to incomplete polarization rotation in the Kerr medium in the open and closed states were 15% and 0.005%, respectively. The use of the gate in a time-resolved fluorescence measurement of DMABN is also demonstrated.
Tyrosines1234-1235 are critical for activation of the tyrosine kinase encoded by the MET proto-oncogene (HGF receptor). (1994)

The tyrosine kinase encoded by the MET proto-oncogene (p190MET) is the receptor for Hepatocyte Growth Factor/Scatter Factor (HGF/SF). Previous work has shown that autophosphorylation of p190MET enhances its enzymatic activity and that the major phosphorylation site is Tyr1235, located in the catalytic domain. This residue is part of a 'three tyrosine' motif, including Tyr1230, Tyr1234, and Tyr1235, conserved in several other receptor kinases. We studied the role of these tyrosines in the positive regulation of the p190MET kinase by site-directed mutagenesis. Substitution of either Tyr1235 or Tyr1234 with phenylalanine severely reduced the in vitro kinase activity toward exogenous substrates. Kinetic experiments showed that the residual activity of these mutants could still be enhanced by autophosphorylation. Phosphopeptide mapping indicated that, in the absence of Tyr1235, Tyr1234 is phosphorylated. Only the replacement of both Tyr1234 and Tyr1235 yielded a mutant which completely lost the ability to be activated by autophosphorylation. In stable transfectants expressing the HGF/SF receptor with single substitution of either Tyr1234 or Tyr1235 the response to HGF/SF was impaired. The ligand did not induce tyrosine phosphorylation of the receptor nor stimulated chemotaxis. These data show that Tyr1234 and Tyr1235 are critical for the activation of the HGF/SF receptor kinase both in vitro and in response to the ligand in intact cells.
Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis (2018)

ctDNA profiles appear to mirror the genomic landscape of metastatic prostate cancer tissue and may cost-efficiently provide somatic information in clinical trials designed to identify predictive biomarkers. However, intronic sequencing of the interrogated tumor suppressors challenges the ubiquitous focus on coding regions and is vital, together with profiling of synchronous white blood cells, to minimize erroneous assignments which in turn may confound results and impede true associations in clinical trials.
High-Efficiency Expression and Solubilization of Functional T Cell Antigen Receptor Heterodimers (1992)

The T cell receptor (TCR) zeta chain was attached to the TCR alpha and beta extracellular domains to induce efficient expression of alpha beta heterodimers that can recognize complexes of antigen with major histocompatibility complex (MHC) molecules. Chimeric constructs expressed in RBL-2H3 cells were efficiently transported to the cell surface uniquely as disulfide-linked heterodimers. Transfectants were activated by specific antigen-MHC complexes, which demonstrated that the expressed alpha beta was functional and that CD3 was not required for antigen-MHC binding. Constructs with thrombin cleavage sites were efficiently cleaved to soluble disulfide-linked heterodimers. Thus, attachment of TCR zeta domains and protease cleavage sites to TCR alpha and beta induces expression of demonstrably functional heterodimers that can be solubilized.
Direct least-squares fitting of algebraic surfaces (1987)

In the course of developing a system for fitting smooth curves to camera input we have developed several direct (i.e. noniterative) methods for fitting a shape (line, circle, conic, cubic, plane, sphere, quadric, etc.) to a set of points, namely exact fit, simple fit, spherical fit, and blend fit. These methods are all dimension-independent, being just as suitable for 3D surfaces as for the 2D curves they were originally developed for.Exact fit generalizes to arbitrary shapes (in the sense of the term defined in this paper) the well-known determinant method for planar exact fit. Simple fit is a naive reduction of the general overconstrained case to the exact case. Spherical fit takes advantage of a special property of circles and spheres that permits robust fitting; no prior direct circle fitters have been as robust, and there have been no previous sphere fitters. Blend fit finds the best fit to a set of points of a useful generalization of Middleditch-Sears blending curves and surfaces, via a nonpolynomial generalization of planar fit.These methods all require (am+bn)n2 operations for fitting a surface of order n to m points, with a = 2 and b = 1/3 typically, except for spherical fit where b is larger due to the need to extract eigenvectors. All these methods save simple fit achieve a robustness previously attained by direct algorithms only for fitting planes. All admit incremental batched addition and deletion of points at cost an2 per point and bn3 per batch.
130-GSa/s photonic analog-to-digital converter with time stretch preprocessor (2002)

In this letter, we demonstrate a photonic analog-to-digital converter with time stretch (TS) preprocessor that has a sampling rate of 130 GSa/s. The system has a signal-to-noise ratio (SNR) exceeding seven effective number of bits over a 1-GHz bandwidth at 18 GHz. We present an analytical model of the SNR in the TS preprocessor which shows that over the specified bandwidth, the SNR is limited by the amplified spontaneous emission beat noise.
Comparative Genomics and Transcriptomics of Propionibacterium acnes (2011)

The anaerobic gram-positive bacterium Propionibacterium acnes is a human skin commensal that is occasionally associated with inflammatory diseases. Recent work has indicated that evolutionary distinct lineages of P. acnes play etiologic roles in disease while others are associated with maintenance of skin homeostasis. To shed light on the molecular basis for differential strain properties, we carried out genomic and transcriptomic analysis of distinct P. acnes strains. We sequenced the genome of the P. acnes strain 266, a type I-1a strain. Comparative genome analysis of strain 266 and four other P. acnes strains revealed that overall genome plasticity is relatively low; however, a number of island-like genomic regions, encoding a variety of putative virulence-associated and fitness traits differ between phylotypes, as judged from PCR analysis of a collection of P. acnes strains. Comparative transcriptome analysis of strains KPA171202 (type I-2) and 266 during exponential growth revealed inter-strain differences in gene expression of transport systems and metabolic pathways. In addition, transcript levels of genes encoding possible virulence factors such as dermatan-sulphate adhesin, polyunsaturated fatty acid isomerase, iron acquisition protein HtaA and lipase GehA were upregulated in strain 266. We investigated differential gene expression during exponential and stationary growth phases. Genes encoding components of the energy-conserving respiratory chain as well as secreted and virulence-associated factors were transcribed during the exponential phase, while the stationary growth phase was characterized by upregulation of genes involved in stress responses and amino acid metabolism. Our data highlight the genomic basis for strain diversity and identify, for the first time, the actively transcribed part of the genome, underlining the important role growth status plays in the inflammation-inducing activity of P. acnes. We argue that the disease-causing potential of different P. acnes strains is not only determined by the phylotype-specific genome content but also by variable gene expression.
Protein-like Activator for n-Alkane Oxidation by Pseudomonas aeruginosa S7B1 (1972)

During the study of the n-alkane oxidation by Pseudomonas aeruginosa S7B1, a nondialysable activator for n-alkane oxidation was discovered in the culture broth of the strain. The activator was purified, as judged by cellulose acetate membrane electrophoresis, by ammonium sulfate precipitation and chromatography on DEAE-Sephadex, CM-Sephadex and Sephadex G-75 columns. The purified activator, which was positive in protein color reactions, remarkable stimulated only the oxidation of n-hexadecane, though it was not observed in case of palmitic acid or glucose oxidation. Co-operative action between the activator and rhamnolipid, which had been isolated as a growth stimulant of P. aeruginosa S7B1 on n-hexadecane by the authors, was observed not only in the oxidation of n-hexadecane but also in the growth on n-hexadecane.
Neurite Outgrowth and Synapse Formation by Identified Leech Neurones in Culture (1987)

After injury, neurones in the central nervous system (CNS) of the leech regenerate with a high degree of specificity. The aim of our experiments has been to study the sequential steps involved in neurite growth and synapse formation using isolated identified neurones in culture. An important requirement for sprouting of leech neurones is the substrate. Neurites grow only slowly and sparsely on polylysine or vertebrate laminin. The extracellular matrix of leech ganglion capsules contains a protease-sensitive factor which can be extracted with urea. With this material as substrate, growth proceeds rapidly in defined medium. Another neurite-promoting substrate is provided by the plant lectin concanavalin A (Con A). The activity of Con A, but not of the capsule matrix factor, is blocked by the Con A-specific hapten methyl alpha-D-mannoside. The morphology and branching pattern of the neurites in culture depend on the specific substrate and on the type of neurone. During stimulation, less Ca2+ uptake occurs into growth cones than in cell bodies. The mechanism of neurite growth seems not to depend on activity-mediated Ca2+ influx or on interactions between neuronal cell surfaces. However, even without profuse outgrowth, electrical and chemical synapses develop between neighbouring neurones. The type of synapse depends predictably on the types of neurones within the cell pair. Since the development of a synapse can be followed with time in culture, the sequential events can each be studied separately for this multi-step process.