gebhart/patrepeval huggingface dataset:
Anchor Structure of Staphylococcal Surface Proteins (1997)

Surface proteins of Staphylococcus aureus are anchored to the cell wall by a mechanism requiring a COOH-terminal sorting signal. Previous work demonstrated that the sorting signal is cleaved at the conserved LPXTG motif and that the carboxyl of threonine (T) is linked to the staphylococcal cell wall. By employing different cell wall lytic enzymes, surface proteins were released from the staphylococcal peptidoglycan and their COOH-terminal anchor structure was revealed by a combination of mass spectrometry and chemical analysis. The results demonstrate that surface proteins are linked to a branched peptide (NH2-Ala-gamma-Gln-Lys-(NH2-Gly5)-Ala-COOH) by an amide bond between the carboxyl of threonine and the amino of the pentaglycine cross-bridge that is attached to the epsilon-amino of lysyl. This branched anchor peptide is amide-linked to the carboxyl of N-acetylmuramic acid, thereby tethering the COOH-terminal end of surface proteins to the staphylococcal peptidoglycan.
Development of a Universal Alkoxyamine for “Living” Free Radical Polymerizations (1999)

Examination of novel alkoxyamines has demonstrated the pivotal role that the nitroxide plays in mediating the “living” or controlled polymerization of a wide range of vinyl monomers. Surveying a variety of different alkoxyamine structures led to α-hydrido derivatives based on a 2,2,5-trimethyl-4-phenyl-3-azahexane-3-oxy, 1, skeleton which were able to control the polymerization of styrene, acrylate, acrylamide, and acrylonitrile based monomers. For each monomer set, the molecular weight could be controlled from 1000 to 200 000 amu with polydispersities typically 1.05−1.15. Block and random copolymers based on combinations of the above monomers could also be prepared with similar control. In comparison with 2,2,6,6-tetramethylpiperidinoxy (TEMPO), these new systems represent a dramatic increase in the range of monomers that can be polymerized under controlled conditions and overcome many of the limitations associated with nitroxide-mediated “living” free radical procedures. Monomer selection and functional group compatibility now approach those of ATRP-based systems.
The WIGGUM gene is required for proper regulation of floral meristem size in Arabidopsis (1998)

The study of cell division control within developing tissues is central to understanding the processes of pattern formation. The floral meristem of angiosperms gives rise to floral organs in a particular number and pattern. Despite its critical role, little is known about how cell division is controlled in the floral meristem, and few genes involved have been identified. We describe the phenotypic effects of mutations in WIGGUM, a gene required for control of cell proliferation in the floral and apical meristem of Arabidopsis thaliana. wiggum flowers contain more organs, especially sepals and petals, than found in wild-type flowers. This organ number phenotype correlates with specific size changes in the early floral meristem, preceding organ initiation. Genetic studies suggest that WIGGUM acts on a similar process but in a separate pathway than the CLAVATA1 and CLAVATA3 genes in meristem size regulation, and reveal interactions with other genes affecting meristem structure and identity. Analysis of double mutant phenotypes also reveals a role for WIGGUM in apical meristem function. We propose that WIGGUM plays a role in restricting cell division relative to cellular differentiation in specific regions of the apical and floral meristems.
An Explosive Demolition, Engineering and Society (2000)

In my younger days around 1965 I read a book tilted 'Red for Danger' by L.T.C. Rolt on rail accidents that have occurred in the United Kingdom. After reading the book I was struck by the similarity of themes in the accidents particularly where set procedures were modified or not followed, and the number of different players or contributors involved. In many cases the 'localised' system had operated for years under these conditions with no accident. No one was the wiser nor did anyone at higher levels inquire or audit the process. The flawed logic appeared to be 'if it is working leave well enough alone'.
Toll-Like Receptors in Health and Disease: Complex Questions Remain (2003)

Until recently, the manner in which we respond to pathogens was obscure. It is now clear that a family of proteins, the Toll-like receptors (TLRs),3 contribute to the signal transduction induced by many pathogen-associated molecular patterns (PAMPs), and perhaps also to endogenous damage signals generated at sites of inflammation. Some TLRs act as central integrators of a wide variety of signals, responding to diverse agonists with an apparently common output, while other members of the family show (to date) considerable specificity with regard to their stimuli. However, many questions remain regarding the immunopharmacology of TLRs, their roles in innate immunity, and their manipulation by pathogens.
Sterols of Chlorella. II. The Occurrence of an Unusual Sterol Mixture in Chlorella vulgaris (1967)

The first identification of a sterol in Chlorella was by Klosty and Bergmann (5) in 1952 when they isolated ergosterol from Chlorella pyrenoidosa. More recently, Otsuka (6) identified ergosterol and a A5 sterol in Chlorella ellipsoidea. Ergosterol was the principal component of the mixture. Recent work in this laboratory has been centered about the identi- fication of sterols from other species of Chlorella. A mixture of the A5 sterols, 'poriferasterol, cliona- sterol, and 22-dihydrobrassicasterol was 'found (7) in C. ellipsoidea and C. saccharophila, but no ergo- sterol was detected. Chlorella vulgaris was shown to contain chondrillasterol as its prin,cipal sterol com- ponent, and although 2 other sterols were present in significant quantities, they were not isolated. Since plant sterols are known to have an effect on animal metajbolism, and algae are being considered as future sources of food, it is important that we know the sterol composition of these algae. This paper de- scribes the isolation and identification of each of the 2 unknown sterols occurring in C. vulgaris. iCells of Chlorella vzlgaris Beyer., Emerson's strain, were grown heterotrophically on 'basal inor- ganic medium containing 0.5 % glucose in 15-liter carboys equipped with bubbling tubes for air (3). The cells were harvested in a Sharples Super Centri- fuge and freeze-dried before extraction. Average yield was 3 grams dry weight per liter. Lipid material was extracted from the cells with acetone in a soxhlet apparatus, saponified under nitrogen, and the non- saponifiable matter extracted with ether in a liquidliquid extraction apparatus. The non-saponifiable lipid was fractionated as described by Hef'tmann et al.
Form, function, and use of retroviral Gag proteins (1991)

From the Department of Biochemistry and Molecular Biology, Louisiana State University Medical Center — Shreveport, Shreveport, Louisiana, USA.
Early Effects of Arterial Hemodynamic Conditions on Human Saphenous Veins Perfused Ex Vivo (2000)

Exposure to the arterial hemodynamic environment is thought to be a potential trigger for the pathological remodeling of saphenous vein grafts. Using matched pairs of freshly isolated human saphenous vein, we analyzed the early effects of ex vivo hemodynamic conditions mimicking the venous (native) compared with arterial (graft) environment on the key components of vascular remodeling, ie, matrix metalloproteinase (MMP)-9 and MMP-2 and cell proliferation. Interestingly, we found that arterial conditions halved latent MMP-9 (50+/-11%, P=0.01) and MMP-2 (44+/-6%, P=0.005) levels relative to matched vein pairs maintained ex vivo under venous perfusion for up to 3 days. Immunostaining supported decreased MMP levels in the innermost area of arterially perfused veins. Either decreased synthesis or increased posttranslational processing may decrease MMP zymogen levels. Biosynthetic radiolabeling showed that arterial perfusion actually increased MMP-9 and MMP-2 production. When we then examined potential pathways for MMP zymogen processing, we found that arterial conditions did not affect the expression of MT-MMP-1, a cell-associated MMP activator, but that they significantly increased the levels of superoxide, another MMP activator, suggesting redox-dependent MMP processing. Additional experiments indicated that increased superoxide under arterial conditions was due to diminished scavenging by decreased extracellular superoxide dismutase. Arterial perfusion also stimulated cell proliferation (by 220% to 750%) in the majority of vein segments investigated. Our observations support the hypothesis that arterial hemodynamic conditions stimulate early vein graft remodeling. Furthermore, physiological arterial flow may work to prevent pathological remodeling, particularly the formation of intimal hyperplasia, through rapid inactivation of secreted MMPs and, possibly, through preferential stimulation of cell proliferation in the outer layers of the vein wall.
Patterning of Plasmonic Nanoparticles into Multiplexed One-Dimensional Arrays Based on Spatially Modulated Electrostatic Potential (2011)

We report a new strategy to pattern plasmonic nanoparticles into multiplexed one-dimensional arrays based on the spatially modulated electrostatic potential. The 32 nm Au nanoparticles can be simultaneously deposited on one chip with tunable interparticle distance by solely adjusting the width of the grooves. Furthermore, 32 and 13 nm Au nanoparticles can be selectively deposited in grooves of different widths on one chip. As a result, the surface plasmon absorption bands on the chip can be tuned depending on the interparticle distance or the particle size of multiplex 1D arrays, which could enhance the Raman scattering cross section of the adsorbed molecules and result in multiplex surface-enhanced Raman scattering (SERS) response on the chip. This strategy provides a general method to fabricate 1D multiplex arrays with different particle sizes and interparticle distances on one chip.
Relationship of the Mayo-Portland Adaptability Inventory to functional outcome and cognitive performance measures (1994)

This study evaluated relationships of the Mayo-Portland Adaptability Inventory (MPAI) to the Disability Rating Scale (DRS), the Ranchos Los Amigos Levels of Cognitive Functioning Scale (Rancho), and cognitive performance measures. The Spearman correlation between the MPAI and the DRS was high (rho = .81). Both the MPAI and the DRS differed significantly among patient groups based on independent Rancho ratings (P <.001 for the Kruskal-Wallis test). Spearman correlations between MPAI scores and cognitive performance measures were generally moderate to good (rho >.40), although cognitive performance measures correlated more highly with MPAI cognitive items than noncognitive items. Contrary to expectation, MPAI noncognitive total score was significantly related to a measure of verbal intelligence, but not to measures of verbal declarative memory. These results suggest the possible importance of the fund of academic and social knowledge and the relatively smaller contribution made by verbal declarative memory to overall functional adaptation after brain injury. Results provide initial evidence of the usefulness and concurrent validity of the MPAI as a measure of adaptive functioning after brain injury.
861. The chemistry of extractives from hardwoods. Part XXVIII. The occurrence of 3 : 4 : 3′ : 5′-tetrahydroxy- and 3 : 4 : 5 : 3′ : 5′-pentahydroxy-stilbene in Vouacapoua species (1956)

F. E. King, T. J. King, D. H. Godson and L. C. Manning, J. Chem. Soc., 1956, 4477 DOI: 10.1039/JR9560004477
Delivering multiple anticancer peptides as a single prodrug using lysyl‐lysine as a facile linker (2007)

A large 40-residue precursor peptide (propeptide 5) was synthesized by linking together four designed anticancer peptide analogs to the neuropeptides: vasoactive intestinal peptide, somatostatin, bombesin and substance P, using enzyme cleavable lysyl-lysine linkers. On incubation with the enzyme trypsin, propeptide 5 was cleaved in a sequence-specific manner at the lysyl-lysine residues in the linker to release the individual peptide fragments which were identified by LC-MS. Another precursor peptide (propeptide 5a), consisting of two of the peptide analogs linked through lysyl-lysine linker, was also preferentially cleaved at the Lys-Lys site on incubation with the enzyme trypsin. Propeptide 5 showed potent anticancer activity, both in vitro and in vivo, which was greater than that of the individual component peptides. The enhanced activity suggests that the propeptide is possibly cleaved in the biological system at the lysyl-lysine site to yield the individual peptide analogs, which together show a synergistic effect. On the basis of these experimental findings, it can be concluded that pairs of basic amino acids such as Lys-Lys can be used as facile linkers for delivering multiple biologically active peptides.
Isolation and cloning fo humCyr 61, a downstream gene in embryonic rhabdomyosarcoma (2000)

The homology between the gene and Gyr61 (A gene could be induced to express by mouse growth factor) was 82% in DNA sequence, and 92% in protein sequence. Among them, Cystein residue and Proline residue highly conserved. This gene was included in cDNA fragments of embryonic rhabdomyosarcoma cel line RD(GenBank Reception Number: Z50168) and benign of prostatic cancer (GenBank Reception Number: Y09859).
Pyruvate accumulation in growth-inhibited cultures of Aerobacter aerogenes (1968)

1. Accumulation of pyruvate occurs during the early stages of exponential growth of aerobic, anaerobic and static cultures of a strain of Aerobacter aerogenes. In normal cultures of this organism the content of pyruvate increases until most of the glucose of the medium has been consumed, and then declines rapidly. The presence of unconsumed sugar is not the sole reason for the accumulation of keto acid, since this is unaffected by the addition of extra glucose to either exponentialphase or stationary-phase cultures. 2. In aminopterin-inhibited cultures, the rate of glucose utilization is decreased greatly, and pyruvate continues to accumulate throughout the period of incubation. This prolonged phase of accumulation appears to be a consequence of the growth inhibition, and not to a specific action of aminopterin on the phosphoroclastic breakdown of pyruvate, since it occurs also when growth is restricted by the antibiotics streptomycin, chloramphenicol and neomycin. 3. A possible explanation is suggested for the accumulation of pyruvate in the inhibited cultures.
Identification of Neutralizing Epitopes within Structural Domain III of the West Nile Virus Envelope Protein (2002)

Using a panel of neutralizing monoclonal antibodies, we have mapped epitopes in domain III of the envelope protein of the New York strain of West Nile virus. The ability of monoclonal antibodies that recognize these epitopes to neutralize virus appeared to differ between lineage I and II West Nile virus strains, and epitopes were located on the upper surface of domain III at residues E307, E330, and E332.
Transport, Separation, and Accumulation of Proteins on Supported Lipid Bilayers (2010)

Transport, separation, and accumulation of proteins in their natural environment are central goals in protein biotechnology. Miniaturized assays of supported lipid bilayers (SLBs) have been proposed as promising candidates to realize such technology on a chip, but a modular system for the controlled transport of membrane proteins does not exist. In this letter, we demonstrate that standing surface acoustic waves drive the in-plane redistribution of proteins on planar SLBs over macroscopic distances (3.5 mm). Accumulation of proteins in periodic patterns of about 10-fold protein concentration difference is accomplished and shown to relax into the homogeneous state by diffusion. Different proteins separate in individual fractions from a homogeneous distribution and are transported and accumulated into clusters using beats. The modular planar setup has the potential of integrating other lab-on-a-chip tools, for monitoring the membrane-protein integrity or adding microfluidic features for blood screening or DNA analysis.
Controlling the Transport Properties of Gold Nanotubule Membranes Using Chemisorbed Thiols (2001)

We have developed a new class of synthetic membranes that consist of a porous polymeric support that contains an ensemble of gold nanotubules that span the complete thickness of the support membrane. The support is a commercially available microporous polycarbonate filter with cylindrical nanoscopic pores. The gold nanotubules are prepared via electroless deposition of Au onto the pore walls; that is, the pores act as templates for the nanotubules. We have shown that by controlling the Au deposition time, Au nanotubules that have effective inside diameters of molecular dimensions (<1 nm) can be prepared. Hence, these membranes are a new class of molecular sieves. In addition, because the tubules are composed of gold, well-known Au-thiol chemistry can be used to change the chemical environment within the tubules. This paper reviews recent research on using chemisorbed thiols to control the transport properties of Au nanotubule membranes. The use of both electrical neutral thiols to introduce chemical-transport selectivity and charged thiols to introduce ion-transport selectivity is reviewed.
Micromagnetic calculations of ferromagnetic resonance in submicron ferromagnetic particles (2002)

Micromagnetic simulations of the ferromagnetic resonance (FMR) spectrum of submicron circular ferromagnetic particles show a number of well-defined absorption peaks as a function of the applied dc magnetic field. In addition to a single large peak due to the uniform mode of precession, smaller peaks are observed on both sides of the uniform mode peak, corresponding to nonuniform or spin-wave modes of precession. The positions of these peaks are a function of particle size. Simulations of the FMR spectrum with and without exchange interactions show that the primary contribution to the energy of the spin-wave modes with absorption peaks at magnetic fields smaller than the uniform mode peak is from exchange interactions, whereas the primary contribution to the energy of the spin-wave modes above the uniform resonance mode arises from dipolar interactions, although all spin-wave modes have some contributions from both types of interactions.
Research on Feature Selection Algorithm in Rough Set Based on Information Entropy (2011)

Rough set theory is an effective approach to imprecision, vagueness, and incompleteness in classification analysis and knowledge discovery .Attribute reduction is a key problem for rough set theory. While computing reduction according to the definitions is a typical NP problem. In this paper, basic concept of rough set theory is presented, one heuristic algorithm for attribution reduction based on conditional entropy is proposed. The actual application shows that the method is feasible and effective.
The program-size complexity of self-assembled squares (extended abstract) (2000)

Article The program-size complexity of self-assembled squares (extended abstract) Share on Authors: Paul W. K. Rothemund Dept. of Computer Science, University of Southern California Dept. of Computer Science, University of Southern CaliforniaView Profile , Erik Winfree Dept. of Computer Science and CNS, California Institute of Technology Dept. of Computer Science and CNS, California Institute of TechnologyView Profile Authors Info & Claims STOC '00: Proceedings of the thirty-second annual ACM symposium on Theory of computingMay 2000 Pages 459–468https://doi.org/10.1145/335305.335358Online:01 May 2000Publication History 251citation994DownloadsMetricsTotal Citations251Total Downloads994Last 12 Months30Last 6 weeks8 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Therapeutic response and side effects of repeated radioligand therapy with 177Lu-PSMA-DKFZ-617 of castrate-resistant metastatic prostate cancer (2016)

Prostate-specific membrane antigen (PSMA) is highly expressed on prostate epithelial cells and strongly up-regulated in prostate cancer (PC), making it an optimal target for the treatment of metastasized PC. Radioligand therapy (RLT) with 177Lu-PSMA-DKFZ-617 (Lu-PSMA) is a targeted therapy for metastatic PC. In this study, we retrospectively analyzed the side effects and the response rate of 24 hormone and/or chemorefractory PC patients with a mean age of 75.2 years (range: 64-82) with distant metastases and progressive disease according to the PSA level, who were treated with Lu-PSMA. Median PSA was 522 ng/ml (range: 17-2360). Forty-six cycles of Lu-PSMA were performed. Of the 24 patients, 22 received two cycles. Eight weeks after the first cycle of Lu-PSMA therapy 79.1% experienced a decline in PSA level. Eight weeks after the second cycle of Lu-PSMA therapy 68.2% experienced a decline in PSA relative to the baseline value. Apart from two cases of grade 3 anemia, there was no relevant hemato- or nephrotoxicity (grade 3 or 4). These results confirmed that Lu-PSMA is a safe treatment option for metastatic PC patients and has a low toxicity profile. A positive response to therapy in terms of decline in PSA occurs in about 70% of patients.
Interfacial gate resistance in Schottky-barrier-gate field-effect transistors (1998)

We discuss in depth a previously overlooked component in the gate resistance R/sub g/ of Schottky-Barrier-Gate FETs, in particular, 0.1-/spl mu/m gate-length AlInAs/GaInAs MODFETs. The high-frequency noise and power gain of these FETs depend critically on R/sub g/. This has been the motivation for the development of T-gates that keep the gate finger metallization resistance R/sub ga/ (proportional to the gate width W/sub g/) low, even for very short gate length L/sub g/. R/sub ga/ increases with frequency due to the skin effect, but our three-dimensional (3-D) numerical modeling shows conclusively that this effect is negligible. We show that the always "larger-than-expected" R/sub g/ is instead caused by a component R/sub gi/ that scales inversely with W/sub g/. We interpret R/sub gi/ as a metal-semiconductor interfacial gate resistance. The dominance of R/sub gi/ profoundly affects device optimization and model scaling. For GaAs and InP-based SBGFETs, there appears to exist a smallest practically achievable normalized interfacial gate resistance r/sub gi/ on the order of 10/sup -7/ /spl Omega/ cm/sup 2/.