gebhart/patrepeval huggingface dataset:
The Copper Active Site of CBM33 Polysaccharide Oxygenases (2013)

The capacity of metal-dependent fungal and bacterial polysaccharide oxygenases, termed GH61 and CBM33, respectively, to potentiate the enzymatic degradation of cellulose opens new possibilities for the conversion of recalcitrant biomass to biofuels. GH61s have already been shown to be unique metalloenzymes containing an active site with a mononuclear copper ion coordinated by two histidines, one of which is an unusual τ-N-methylated N-terminal histidine. We now report the structural and spectroscopic characterization of the corresponding copper CBM33 enzymes. CBM33 binds copper with high affinity at a mononuclear site, significantly stabilizing the enzyme. X-band EPR spectroscopy of Cu(II)-CBM33 shows a mononuclear type 2 copper site with the copper ion in a distorted axial coordination sphere, into which azide will coordinate as evidenced by the concomitant formation of a new absorption band in the UV/vis spectrum at 390 nm. The enzyme's three-dimensional structure contains copper, which has been photoreduced to Cu(I) by the incident X-rays, confirmed by X-ray absorption/fluorescence studies of both aqueous solution and intact crystals of Cu-CBM33. The single copper(I) ion is ligated in a T-shaped configuration by three nitrogen atoms from two histidine side chains and the amino terminus, similar to the endogenous copper coordination geometry found in fungal GH61.
A knowledge-based approach for textual information extraction from mixed text/graphics complex document images (2010)

A new knowledge-based technique for extracting and identifying text-lines from various real-life mixed text/graphics complex document images is presented in this paper. The proposed technique first decompose the document image into distinct object planes to separate homogeneous objects including textual regions of interest, non-text objects such as graphics and pictures, and background textures. Then a knowledge-based text extraction and identification method is performed on the resultant planes to obtain text-lines with different characteristics in each plane. This proposed system can offer high flexibility and expandability by just updating new rules for coping with more various types of real-life and future complex document images. From the experimental and comparative results, the proposed knowledge-based technique demonstrates its effectiveness and advantages on extracting text-lines with various illuminations, sizes, and font styles from various types of mixed text/graphics complex document images.
Comparison of charged derivatives for high energy collision-induced dissociation tandem mass spectrometry (1995)

Fixed-charge derivatives have been used to direct the fragmentation pattern of high energy collision-induced dissociation tandem mass spectra for several years. It has been noted that a fixed-charge placed at a terminus of a peptide will simplify the pattern of fragment ions that are produced in collision-induced dissociation. Trimethylammoniumacetyl, dimethyloctylammoniumacetyl, and triphenylphosphoniumethyl derivatives have been cited in the literature for this purpose and many other structures are possible. This work compares the cited derivatives as well as some new structures. The criteria used include the ease of synthesis and purification of the derivatized peptide and the effects of the derivative on the peptide sequence fragment ion yield and ionization efficiency. The trimethylammoniumacetyl derivative is concluded to be the most practical for general use, whereas the dimethyloctylammoniumacetyl derivative is found to be desirable for use with hydrophilic peptides.
CD133 positive hepatocellular carcinoma cells possess high capacity for tumorigenicity (2007)

Recently increasing reported data have suggested that only a small subset of cancer cells possess capability to initiate malignancies including leukemia and solid tumors, which was based on investigation in these cells displaying a distinct surface marker pattern within the primary cancers. CD133 is a putative hematopoietic and neuronal stem-cell marker, which was also considered as a tumorigenic marker in brain and prostate cancer. We hypothesized that CD133 was a marker closely correlated with tumorigenicity, since it was reported that CD133 expressed in human fetal liver and repairing liver tissues, which tightly associated with hepatocarcinogenesis. Our findings showed that a small population of CD133 positive cells indeed exists in human hepatocellular carcinoma (HCC) cell lines and primary HCC tissues. From SMMC-7721 cell line, CD133+ cells isolated by MACS manifested high tumorigenecity and clonogenicity as compared with CD133- HCC cells. The implication that CD133 might be one of the markers for HCC cancer stem-like cells needed further investigation.
TMEM106B, the Risk Gene for Frontotemporal Dementia, Is Regulated by the microRNA-132/212 Cluster and Affects Progranulin Pathways (2012)

Frontotemporal lobar degeneration with TDP-43 inclusions (FTLD-TDP) is a fatal neurodegenerative disease with no available treatments. Mutations in the progranulin gene (GRN) causing impaired production or secretion of progranulin are a common Mendelian cause of FTLD-TDP; additionally, common variants at chromosome 7p21 in the uncharacterized gene TMEM106B were recently linked by genome-wide association to FTLD-TDP with and without GRN mutations. Here we show that TMEM106B is neuronally expressed in postmortem human brain tissue, and that expression levels are increased in FTLD-TDP brain. Furthermore, using an unbiased, microarray-based screen of >800 microRNAs (miRs), we identify microRNA-132 as the top microRNA differentiating FTLD-TDP and control brains, with <50% normal expression levels of three members of the microRNA-132 cluster (microRNA-132, microRNA-132*, and microRNA-212) in disease. Computational analyses, corroborated empirically, demonstrate that the top mRNA target of both microRNA-132 and microRNA-212 is TMEM106B; both microRNAs repress TMEM106B expression through shared microRNA-132/212 binding sites in the TMEM106B 3'UTR. Increasing TMEM106B expression to model disease results in enlargement and poor acidification of endo-lysosomes, as well as impairment of mannose-6-phosphate-receptor trafficking. Finally, endogenous neuronal TMEM106B colocalizes with progranulin in late endo-lysosomes, and TMEM106B overexpression increases intracellular levels of progranulin. Thus, TMEM106B is an FTLD-TDP risk gene, with microRNA-132/212 depression as an event which can lead to aberrant overexpression of TMEM106B, which in turn alters progranulin pathways. Evidence for this pathogenic cascade includes the striking convergence of two independent, genomic-scale screens on a microRNA:mRNA regulatory pair. Our findings open novel directions for elucidating miR-based therapies in FTLD-TDP.
Properties of two classes of rat brain acidic amino acid receptors induced by distinct mRNA populations in Xenopus oocytes (1988)

The Xenopus laevis oocyte expression system was used to study the molecular composition of mRNAs encoding acidic amino acid (AA) receptors from rat brain. Xenopus oocytes injected with poly(A) mRNA express two general classes of AA receptors. One class consists of AA-gated cation channels. Responses are evoked by N-methyl-D-aspartate (NMDA), by kainate, and to a lesser extent by L-glutamate or quisqualate. The second class of receptor is coupled to an intracellular second messenger pathway activating an oocyte-encoded Ca2+-activated Cl- conductance. This second messenger-coupled AA receptor can be activated by L-glutamate or quisqualate. DL-2-amino-5-phosphonopentanoic acid and D-alpha-aminohexanedioic acid inhibit the AA-gated cation conductances activated by NMDA or kainate with different potencies but do not inhibit the second messenger-coupled AA receptor. Responses to NMDA are enhanced by micromolar level of glycine and are inhibited by Mg2+, Zn2+, or MK-801. Dose-response analysis reveals that the AA-gated cation conductance activated by kainate requires the binding of two agonist molecules. To study the molecular composition, the mRNAs were size-fractionated by denaturing agarose gel electrophoresis. About 20-fold purification in specific activity (nA/ng of mRNA injected) of mRNAs encoding the second messenger-coupled AA receptor was achieved. In contrast, only a slight enrichment of the mRNAs encoding the AA-gated channel was observed. This suggests that the second messenger-coupled AA receptor is encoded by a single size class of mRNA, whereas the AA-gated cation channel(s) is encoded by multiple species of mRNAs or by mRNAs whose size distribution is heterogeneous.
Comparison of Styrene with Methyl Methacrylate Copolymers on the Adhesive Performance and Peeling Master Curves of Acrylate Pressure Sensitive Adhesives (2005)

Abstract Summary: Styrene (S) and methyl methacrylate (MMA) copolymers were prepared with acrylates, such as butyl acrylate, 2‐ethylhexyl acrylate and acrylic acid, for application as pressure sensitive adhesives (PSA). The copolymer compositions were designed to provide constant glass transition temperature. The PSA were tested using peel adhesion resistance, static shear resistance, loop tack and DMA. Time‐temperature‐superposition (TTS) was used to construct peel resistance master curves to compare copolymers containing S and MMA, and obtain a structural interpretation of the PSA performance. The TTS master curves were combined for related copolymer series to obtain composition super master curves. The super master curve construction demonstrated the comonomer composition dependence of the PSA performance and distinguished copolymers containing S from those containing MMA. Composition related performance was exhibited by static shear and loop tack, the latter in relation to the concentration shift factors. DMA results confirmed the adhesive performance interpretations. Composition super master curves suggested differences in the relative mobility of S and MMA copolymers. Chain branching and entanglements were more significant with MMA than with S copolymers. DMA and static shear resistance confirmed the peel resistance results. S copolymers decreased the loop tack consistent with their higher molecular weight and lower polydispersity, with fewer low molecular weight fractions contributing to the tack. MMA copolymers dissipated more energy under high stress than S copolymers. Example peel master curve for formulation AA4M91‐2 (reference temperature: T 0 = 298 K). magnified image Example peel master curve for formulation AA4M91‐2 (reference temperature: T 0 = 298 K).
Surface-associated proteins of Staphylococcus aureus: Their possible roles in virulence (1994)

A class of proteins that are associated with the cell surface of Gram-positive bacteria has been recognised. Common structural features which are implicated in the proper secretion and attachment of these proteins to the cell surface occur in the C-termini. N-terminal domains interact with the host by binding to soluble host proteins, to matrix proteins or to host cells. They probably have important roles in pathogenicity by allowing bacteria to avoid host defences and by acting as adhesins. Four such proteins of Staphylococcus aureus have been characterised: protein A (immunoglobulin binding protein), fibronectin binding proteins, collagen binding protein and the fibrinogen binding protein (clumping factor). Site-specific mutants are being used to define their roles in pathogenesis in in vitro and in vivo models of adherence and infection.
Mode-locked lasers with nonlinear external cavities (1988)

A nonlinear element, when introduced into an external cavity, is shown to improve the mode locking of lasers. Mode locking is achieved by inducing coupling between the cavity modes, thus permitting more efficient transmission of phase information. We begin by discussing a phenomenological laser model for homogeneously broadened systems. The model laser is coupled to an external cavity and contains a nonlinear element. The returning pulse from this external cavity is then mixed with a circulating pulse in the laser at the output mirror. We have considered two nonlinear elements, a saturable absorber and a saturable amplifier. Although these elements have quite different pulse-shaping effects, they both cause considerable improvement in mode-locked performance.
Monolithic integration of InGaAs/InAlAs MODFETs and RTDs on InP-bonded-to Si substrate (2003)

The authors report the monolithic integration of InGaAs/InAlAs MODFETs and RTDs MBE grown using selective epitaxy on InP which has been bonded to a silicon substrate. The study demonstrates the feasibility of monolithically integrating III-V devices having different heterostructures with silicon devices.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Polymerization of 1-hexene catalyzed by bis(cyclopentadienyl)zirconium dichloride/methylaluminoxane; effect of temperature on the molecular weight and the microstructure of poly(1-hexene) (1998)

Polymerization of 1-hexene catalyzed with bis(cyclopentadienyl)zirconium dichloride/methyl-aluminoxane revealed increasing molecular weight with decreasing polymerization temperature. The Arrhenius plot (lg M̄n vs. 1/T) shows a sigmoidal curve. These results were interpreted in the sense of a change in the nature of the active species with temperature. In addition it was observed that with decreasing polymerization temperature the concentration of isotactic sequences increases.
Adaptive correction of depth‐induced aberrations in multiphoton scanning microscopy using a deformable mirror (2002)

We demonstrate adaptive aberration correction for depth-induced spherical aberration in a multiphoton scanning microscope with a micromachined deformable mirror. Correction was made using a genetic learning algorithm with two-photon fluorescence intensity feedback to determine the desired shape for an adaptive mirror. For a 40x/0.6 NA long working distance objective, the axial scanning range was increased from 150 mm to 600 mm.
A quantitative test to estimate neutralizing antibodies to the hepatitis C virus: cytofluorimetric assessment of envelope glycoprotein 2 binding to target cells. (1996)

Hepatitis C virus (HCV) is a major cause of chronic hepatitis. The virus does not replicate efficiently in cell cultures, and it is therefore difficult to assess infection-neutralizing antibodies and to evaluate protective immunity in vitro. To study the binding of the HCV envelope to cell-surface receptors, we developed an assay to assess specific binding of recombinant envelope proteins to human cells and neutralization thereof. HCV recombinant envelope proteins expressed in various systems were incubated with human cells, and binding was assessed by flow cytometry using anti-envelope antibodies. Envelope glycoprotein 2 (E2) expressed in mammalian cells, but not in yeast or insect cells, binds human cells with high affinity (Kd approximately 10(-8) M). We then assessed antibodies able to neutralize E2 binding in the sera of both vaccinated and carrier chimpanzees, as well as in the sera of humans infected with various HCV genotypes. Vaccination with recombinant envelope proteins expressed in mammalian cells elicited high titers of neutralizing antibodies that correlated with protection from HCV challenge. HCV infection does not elicit neutralizing antibodies in most chimpanzees and humans, although low titers of neutralizing antibodies were detectable in a minority of infections. The ability to neutralize binding of E2 derived from the HCV-1 genotype was equally distributed among sera from patients infected with HCV genotypes 1, 2, and 3, demonstrating that binding of E2 is partly independent of E2 hypervariable regions. However, a mouse monoclonal antibody raised against the E2 hypervariable region 1 can partially neutralize binding of E2, indicating that at least two neutralizing epitopes, one of which is hypervariable, should exist on the E2 protein. The neutralization-of-binding assay described will be useful to study protective immunity to HCV infection and for vaccine development.
Evaluation of MK filters for recovery of enteroviruses from tap water (1994)

The MK filter is an electropositively charged filter that can be used to concentrate enteroviruses from large volumes (400 to 1,000 liters) of water. This filter is less expensive than the commonly used 1MDS electropositive filter. In this study, we compared the recovery of poliovirus 1 (PV1) and that of coxsackievirus B3 (CB3) from 378 liters of tap water, using both the MK and the 1MDS filters. Viruses were eluted from the filters with 3% beef extract buffered with 0.05 M glycine (pH 9.5) and reconcentrated via organic flocculation. At high virus inputs (approximately 10(6) PFU), the overall recovery (after elution and reconcentration) of PV1 and CB3 from tap water with the MK filter was less than that achieved with the 1MDS filter (P < 0.05). The recoveries of PV1 from tap water with the MK and 1MDS filters were 73.2% +/- 26% (n = 5 trials) and 90.2% +/- 5.9% (n = 5 trials), respectively. The recoveries of CB3 from tap water with the MK and 1MDS filters were 32.8% +/- 34.5% (n = 4 trials) and 95.8% +/- 12.0% (n = 4 trials), respectively. This study indicated that the MK filter consistently provided lower recovery, with wider variability, of PV1 and CB3 from tap water than the 1MDS filter.
High cell density media for Escherichia coli are generally designed for aerobic cultivations – consequences for large-scale bioprocesses and shake flask cultures (2008)

The accumulation of formate in oxygen limited cultivations of E. coli can be fully prevented by addition of the trace elements selenium, nickel and molybdenum, necessary for the function of FHL complex. For large-scale cultivations, if glucose gradients are likely, the results from the two-compartment scale-down bioreactor indicate that the addition of the extra trace elements is beneficial. No negative effects on the biomass yield or on any other bioprocess parameters could be observed in cultures with the extra trace elements if the cells were repeatedly exposed to transient oxygen limitation.
Comparison of the fragmentation produced by fast atom bombardment and photodissociation of peptides (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTComparison of the fragmentation produced by fast atom bombardment and photodissociation of peptidesCarlito B. Lebrilla, Diana T. S. Wang, Tadashi J. Mizoguchi, and Robert T. McIver Jr.Cite this: J. Am. Chem. Soc. 1989, 111, 23, 8593–8598Publication Date (Print):November 1, 1989Publication History Published online1 May 2002Published inissue 1 November 1989https://pubs.acs.org/doi/10.1021/ja00205a006https://doi.org/10.1021/ja00205a006research-articleACS PublicationsRequest reuse permissionsArticle Views116Altmetric-Citations35LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Stable Low-Pressure Hydrogen Clusters Stored in a Binary Clathrate Hydrate (2004)

Thermodynamic, x-ray diffraction, and Raman and nuclear magnetic resonance spectroscopy measurements show that clusters of H2 can be stabilized and stored at low pressures in a sII binary clathrate hydrate. Clusters of H2 molecules occupy small water cages, whereas large water cages are singly occupied by tetrahydrofuran. The presence of this second guest component stabilizes the clathrate at pressures of 5 megapascals at 279.6 kelvin, versus 300 megapascals at 280 kelvin for pure H2 hydrate.
In Situ Deposition and Patterning of Single‐Walled Carbon Nanotubes by Laminar Flow and Controlled Flocculation in Microfluidic Channels (2005)

Well-defined patterns of single-walled carbon nanotubes (SWNTs) with controlled density and alignment were produced by using controlled flocculation in multistream laminar microfluidic networks (see picture). Complex, well-defined SWNT patterns could be generated by control of flow and substrate conditions.
Intraoperative Assessment of Aneurysm Clipping Using Magnetic Resonance Angiography and Diffusion-weighted Imaging: Technical Case Report (2002)

For the first time, intraoperative magnetic resonance imaging has been used to monitor the surgical treatment of a patient with an intracranial aneurysm.
Physical and Chemical Studies on Ceruloplasmin (1970)

Abstract The survival time in plasma of incompletely desialylated ceruloplasmin, labeled with 64Cu or with tritium, was studied in the rat. Removal of less than 20% of the terminal sialic acid, with consequent exposure of the penultimate galactosyl residues, resulted in the rapid disappearance from the circulation of more than 50% of the injected dose. Statistical analysis of the experimental results by means of the Poisson distribution equation supports the estimate that the exposure of no more than 2 galactosyl residues is sufficient to effect prompt clearance of ceruloplasmin from the circulation. Examination of the specificity of the two neuraminidase preparations used in this study revealed that each of the enzymes possessed a preferential affinity for different sialic acid residues, although the results from each were statistically predictable. Consequently, the removal of any 2 sialic acid residues from 1 molecule of ceruloplasmin appears to be incompatible with the continued survival of that molecule in the circulation.