gebhart/patrepeval huggingface dataset:
The role of neutrophil membrane glycoprotein GP-150 in neutrophil adherence to endothelium in vitro (1985)

We have previously described two patients with a congenital defect in neutrophil function characterized by an inability to form pus. The patients' neutrophils lack a membrane glycoprotein of mol wt 150,000 daltons (GP-150) on analysis by SDS-PAGE. This glycoprotein is part of a membrane antigen complex recognized by the murine monoclonal antibody (MoAb) 60.3. Addition of MoAb 60.3 to normal neutrophils produces defects in chemotaxis and phagocytosis in vitro similar to those observed in the patients. Since neutrophil adherence to vascular endothelium is prerequisite to neutrophil emigration in vivo, we examined the interaction of the patients' neutrophils and normal neutrophils treated with MoAb 60.3 with cultured endothelium. Adherence was determined as the percentage of 51Cr-labeled purified peripheral blood neutrophils which remained adherent to plastic wells or endothelial monolayers after a 45-minute incubation at 37 degrees C. The percentage of neutrophils from patient 1 remaining adherent to uncoated, fibronectin-coated, or laminin-coated plastic was similar to that observed in normal neutrophils (55% to 84% adherence with normal neutrophils v 73% to 78% adherence with the patient's neutrophils and 63% to 82% adherence with MoAb 60.3-treated normal neutrophils). The adherence of the neutrophils from patient 1 and MoAb 60.3-treated normal neutrophils to human or bovine endothelium in serum-free medium was also not significantly different from that observed in normal neutrophils (less than 10% adherence with normal, MoAb 60.3-treated, and patient neutrophils). In medium containing 10% autologous or heterologous human plasma, however, the adherence of neutrophils from patient 1 or MoAb 60.3-treated normal neutrophils to endothelial monolayers was significantly reduced (35% +/- 7% of normal neutrophils in seven experiments). Although phorbol myristate acetate (PMA) (10 ng/mL) and calcium ionophore A23187 (10(-5) mol/L) markedly increased the adherence of normal neutrophils to endothelial monolayers in serum-free medium (40% to 85% adherence), neither agent increased the adherence of the neutrophils from patient 1 or normal neutrophils treated with MoAb 60.3 (less than 5% adherence). The adherence of PMA-activated neutrophils from patient 2 to endothelial monolayers was also markedly decreased when compared with that of normal neutrophils. Postsecretory cell-free supernatants from PMA-activated normal neutrophils failed to augment adherence of neutrophils from patient 1 (less than 5% adherence).(ABSTRACT TRUNCATED AT 400 WORDS)
A traffic control algorithm in diverse home networks through priority reassignment (2003)

In recent years, many families have personal computers (PCs) and use the Internet service with high-speed modems. So providing high quality network services and connecting home devices together in a network are main issues in home networking. As the need of functional factors is increased in the home network, it is obvious that the home network data traffic have increased as well. For that reason, a key technology of home network services is how to manage the traffic and provide efficient data services between a wide area network (WAN) and home networks, and also within diverse home networks. There are mainly three data traffic types in the home network: control data traffic, Internet/non-real-time data, and multimedia data (include non-real-time and real-time multimedia data). To manage these kinds of traffic, we design a priority-based traffic control scheme and propose an efficient and adaptive traffic control algorithm through priority reassignment.
Melatonin reduces stress‐activated/mitogen‐activated protein kinases in spinal cord injury (2008)

Permanent functional deficits following spinal cord injury (SCI) arise from both mechanical injury and from secondary tissue reactions involving inflammation. The mitogen-activated protein kinases (MAPKs) play a critical role in cell signaling and gene expression. MAPK family includes three major members: extracellular signal regulated kinase (ERK), p38, and c-Jun N-terminal kinase (JNK), representing three different signaling cascades. Moreover, various studies have clearly shown that high-mobility group box 1 (HMGB1) protein is implicated as a putative danger signal involved in the pathogenesis of a variety of inflammatory conditions including autoimmunity, cancer, trauma and hemorrhagic shock, and ischemia-reperfusion injury. Recently, we have reported that the pineal secretory product melatonin exerts important anti-inflammatory effects in an experimental model of SCI induced by the application of vascular clips (force of 24 g) to the dura after a four-level T5-T8 laminectomy. However, no reports are available on the effect of melatonin on MAPK signaling pathways and HMGB1 expression in SCI. The aim of the present study was to evaluate whether the melatonin protective effect observed in SCI is related to the regulation of MAPK signaling pathways and HMGB1 in mice. In this study we demonstrate the efficacy of treatment with the melatonin in SCI in mice in reducing (a) motor recovery, (b) activation of MAPKs p38, JNK and ERK1/2, (c) tumor necrosis factor-alpha expression, and (d) expression of HMGB1. We propose that melatonin's ability to reduce SCI in mice is also related to a reduction in MAPK signaling pathways and HMGB1 expression.
SphK1 and SphK2, Sphingosine Kinase Isoenzymes with Opposing Functions in Sphingolipid Metabolism (2005)

The potent sphingolipid metabolite sphingosine 1-phosphate is produced by phosphorylation of sphingosine catalyzed by sphingosine kinase (SphK) types 1 and 2. In contrast to pro-survival SphK1, the putative BH3-only protein SphK2 inhibits cell growth and enhances apoptosis. Here we show that SphK2 catalytic activity also contributes to its ability to induce apoptosis. Overexpressed SphK2 also increased cytosolic free calcium induced by serum starvation. Transfer of calcium to mitochondria was required for SphK2-induced apoptosis, as cell death and cytochrome c release was abrogated by inhibition of the mitochondrial Ca(2+) transporter. Serum starvation increased the proportion of SphK2 in the endoplasmic reticulum and targeting SphK1 to the endoplasmic reticulum converted it from anti-apoptotic to pro-apoptotic. Overexpression of SphK2 increased incorporation of [(3)H]palmitate, a substrate for both serine palmitoyltransferase and ceramide synthase, into C16-ceramide, whereas SphK1 decreased it. Electrospray ionizationmass spectrometry/mass spectrometry also revealed an opposite effect on ceramide mass levels. Importantly, specific down-regulation of SphK2 reduced conversion of sphingosine to ceramide in the recycling pathway and conversely, down-regulation of SphK1 increased it. Our results demonstrate that SphK1 and SphK2 have opposing roles in the regulation of ceramide biosynthesis and suggest that the location of sphingosine 1-phosphate production dictates its functions.
Cytoskeleton-Plasma Membrane-Cell Wall Continuum in Plants. Emerging Links Revisited (2003)

Eukaryotic cells typically deviate from spherical shapes due to complex interactions between elements of their cytoskeleton and the extracellular matrix (ECM). Communication between the cytoskeleton and ECM is one of the most characteristic features of cellular mechanics and allows cells to respond
Identification of a tyrosinase epitope recognized by HLA-A24-restricted, tumor-infiltrating lymphocytes (1995)

A number of Ags recognized by class I-restricted, melanoma-specific T cells have recently been identified. In this report we demonstrated that tumor-infiltrating lymphocytes (TIL) from melanoma patient 1413 recognize a tumor Ag, tyrosinase, in the context of HLA-A24. This Ag had previously been shown to be recognized by an HLA-A24-restricted TIL, TIL 888, as well as HLA-A2-restricted, melanoma-specific T cells isolated from two additional patients. The peptide epitope recognized by TIL 1413 was then identified through the use of sequential deletions of the tyrosinase cDNA, as well as through prediction of HLA-A24 binding peptides based on a previously identified motif. Two peptides, a 9-amino acid peptide (AFLPWHRLF) and an overlapping 10-amino acid peptide (AFLPWHRLFL) containing an additional leucine at the carboxyl terminus, were both recognized by TIL 1413. Anti-peptide-specific CTL could be induced by repeated stimulation of peripheral blood lymphocytes from melanoma patient 1413, and this CTL line specifically recognized both HLA-A24+ B cell lines pulsed with the peptide and HLA-A24+ tyrosinase+ melanoma cells. This peptide thus represents a reagent that may be used to generate melanoma-specific T cells for adoptive immunotherapy, as well as in peptide vaccines for HLA-A24+ melanoma patients.
Normal Replication of Vesicular Stomatitis Virus without C Proteins (1996)

The expression of two small basic proteins (C and C') encoded by a second open reading frame of the New Jersey serotype of vesicular stomatitis virus (VSV) P gene was reported previously (Spiropoulou and Nichol, J. Virol., 67, 3103-3110, 1993). Here we found that the Indiana serotype virus also expressed C and C' proteins from this reading frame. We eliminated C and C' expression by making a single base change that introduced a stop codon in the C and C' coding sequence, but left the P-protein sequence unchanged. This mutated P gene supported normal replication and packaging of VSV minigenomes encoding G and M proteins. The mutated P gene was also recombined into an infectious clone of VSV that was used to recover virus. The mutant virus no longer expressed the C and C' proteins but showed growth kinetics identical to wild-type virus. The amounts of viral mRNAs and proteins synthesized were indistinguishable in mutant and wild-type virus infected cells as were the yields and composition of mutant and wild-type virus particles. The kinetics of host protein-synthesis shut-off were also identical for both viruses. Although the C and C' proteins were dispensable for VSV growth in tissue culture, they are known to be conserved in all vesiculoviruses, and thus perhaps play a role in viral pathogenesis or transmission by insect vectors.
Worldwide Prevalence of Antimicrobial Resistance inStreptococcus pneumoniae, Haemophilus influenzae,andMoraxella catarrhalisin the SENTRY Antimicrobial Surveillance Program, 1997–1999 (2001)

The in vitro activities of numerous antimicrobials against clinical isolates of Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis from patients with bloodstream and respiratory tract infections in the United States, Canada, Europe, Latin America, and the Asia-Pacific region were studied in the SENTRY Antimicrobial Surveillance Program. Penicillin resistance (minimum inhibitory concentration, > or =2 microg/mL) was noted in all 5 geographic regions, and a high and increasing rate of macrolide resistance among S. pneumoniae isolates was observed. Elevated rates of resistance to clindamycin, trimethoprim-sulfamethoxazole, chloramphenicol, and tetracycline were seen. beta-Lactamase-mediated resistance in H. influenzae to amoxicillin and variable trimethoprim-sulfamethoxazole resistance by region were documented. Resistance to several drugs continues to emerge among pneumococci worldwide, but more stable resistance patterns have been noted for H. influenzae and M. catarrhalis. Continued surveillance of this pathogen group appears to be prudent.
Cell Wall, Cell Membrane, and Volatile Metabolism Are Altered by Antioxidant Treatment, Temperature Shifts, and Peel Necrosis during Apple Fruit Storage (2013)

The transition from cold storage to ambient temperature alters apple quality through accelerated softening, flavor and color changes, and development of physiological peel disorders, such as superficial scald, in susceptible cultivars. To reveal global metabolism associated with this transition, the ‘Granny Smith’ peel metabolome was evaluated during storage of 6 months and shelf life periods. Treatment with the antioxidant diphenylamine (DPA) reduced scald, creating a metabolic contrast with untreated fruit, which developed superficial scald. Superficial scald symptoms developed on control fruit after 120 days of storage, and symptoms progressed following transition to ambient-temperature shelf life. The metabolic profile of control and DPA-treated fruit was divergent after 30 days of cold storage due to differing levels of α-farnesene oxidation products, methyl esters, phytosterols, and other compounds potentially associated with chloroplast integrity and oxidative stress response. Hierarchical cluster analysis revealed coregulation within the volatile synthesis pathway including control of the availability of methyl, propyl, ethyl, acetyl, and butyl alcohol and/or acid moieties for ester biosynthesis. Overall, the application of metabolomics techniques lends new insight into physiological processes leading to cell death and ripening processes that affect fruit flavor, appearance, and overall quality.
Deduced protein sequence of bone small proteoglycan I (biglycan) shows homology with proteoglycan II (decorin) and several nonconnective tissue proteins in a variety of species (1989)

The small proteoglycans (PG) of bone consist of two different molecular species: one containing one chondroitin sulfate chain (PG II) and the other, two chains (PG I). These two proteoglycans are found in many connective tissues and have Mr = 45,000 core proteins with clear differences in their NH2-terminal sequences. Using antisera produced against synthetic peptides derived from the human PG I and PG II NH2 termini, we have isolated several cDNA clones from a lambda gt11 expression library made against mRNA isolated from human bone-derived cells. The clones, which reacted with antisera to the PG II peptide, were sequenced and found to be identical with the PG II class of proteoglycan from human fibroblasts known as PG-40 or decorin. The clones reacting to the PG I antisera, however, had a unique sequence. The derived protein sequence of PG I showed sufficient homology with the PG II sequence (55% of the amino acids are identical, with most others involving chemically similar amino acid substitutions) to strongly suggest that the two proteins were the result of a gene duplication. PG II (decorin) contains one attached glycosaminoglycan chain, while PG I probably contains two chains. For this reason, we suggest that PG I be called biglycan. The biglycan protein sequence contains 368 residues (Mr = 42,510 for the complete sequence and Mr = 37,983 for the secreted form) that appears to consist predominantly of a series of 12 tandem repeats of 24 residues. The repeats are recognized by their conserved leucines (and leucine-like amino acids) in positions previously reported for a diverse collection of proteins (none of which is thought to be proteoglycans) including: two morphogenic proteins (toll and chaoptin) in the fruit fly; a yeast adenylate cyclase; and two human proteins, the von Willebrand Factor-binding platelet membrane protein, GPIb, and a rare serum protein, leucine-rich glycoprotein.
Precision Positioning of Wafer Scanners Segmented Iterative Learning Control for Nonrepetitive Disturbances (2007)

Photolithography is a step in semiconductor manufacturing that uses a laser beam to transfer a pattern from a mask to the surface of a silicon wafer. This process is implemented by an optomechanical device called a wafer scanner (Figure 1). A schematic of the major subsystems of a wafer scanner is shown in Figure 2. The illumination system consists of an argon-fluoride (Ar-F) or similar laser source that passes a laser beam through the photomask mounted on the reticle to form an image of the integrated circuit (IC) on the silicon wafer mounted on the wafer stage. The reduction lens assembly projects a reduced image of the photomask, shown in Figure 3, onto a photoresist layer on the silicon wafer, shown in Figure 4. Linear motors are used to position the wafer and reticle scanning stages relative to the projection lens and illumination system. Although several individual ICs are typically made from a single silicon wafer, the scanner exposes only a small part of the wafer to the laser beam in a single scan. The scan is performed by simultaneously moving the wafer and reticle stages in opposite directions, which reduces the time required for a single scan, while keeping peak velocities of both stages small. After the length of the reticle is scanned, the stages are stepped to the required positions for the scan process at another location on the wafer. This step and scan process is illustrated in Figure 5. The critical dimension (CD) of the IC manufacturing process is the finest line resolvable on the silicon wafer by the scanner. The CD of the scanner depends on the type of optical assembly, laser source, and positioning accuracies of the wafer and reticle stages. State-of-the-art scanners using Ar-F lasers can achieve CDs as small as 65 nm. In addition to the CD, the standard deviation of line size is a performance metric for the wafer scanner. This metric, called the alignment accuracy, indicates how close two features can be reliably placed on the silicon wafer. One of the
An integrated family of amino acid sequence analysis programs (1988)

During the last years abundant sequence data has become available due to the rapid progress in protein and DNA sequencing techniques. The exact three-dimensional structures, however, are available only for a fraction of proteins with known sequences. For many purposes the primary amino acid sequence of a protein can be directly used to predict important structural parameters. However, mathematical presentation of the calculated values often makes interpretation difficult, especially if many proteins must be analysed and compared. Here we introduce a broad-based, user-defined analysis of amino acid sequence information. The program package is based on published algorithms and is designed to access standard protein data bases, calculate hydropathy, surface probability and flexibility values and perform secondary structure predictions. The data output is in an 'easy-to-read' graphic format and several parameters can be superimposed within a single plot in order to simplify data interpretations. Additionally, this package includes a novel algorithm for the prediction of potential antigenic sites. Thus the software package presented here offers a powerful means of analysing an amino acid sequence for the purpose of structure/function studies as well as antigenic site analyses. These algorithms were written to function in context with the UWGCG (University of Wisconsin Genetics Computer Group) program collection, and are now distributed within that package.
Characterization of Small-Diameter Carbon Nanotubes and Carbon Nanocaps on SiC(0001) Using Raman Spectroscopy (2006)

The Raman spectra of carbon nanotubes (CNTs) formed on a 6H–SiC(0001) C-face substrate by surface decomposition were acquired using a 1064 nm Nd:YAG laser as the excitation source. Intense radial-breathing-mode Raman bands were successfully detected under resonant excitation from CNTs formed by the surface decomposition of SiC. Fine CNTs having diameters between 0.7 and 1.3 nm were observed on SiC after heating at 1700 °C in a vacuum electric furnace. These diameters are considerably smaller than those previously observed for CNTs grown by this technique.
Nanocrystal gold molecules (1996)

Gold nanocrystals passivated by self‐assembled monolayers of straightchain alkylhiolate molecules have been obtained as highly purified molecular materials of high intrinsic stability. Evidence is presented for a predicted discrete sequence of energetically optimal fcc structures of a truncated octahedral morphological motif (see cover). The nanocrystal materials have a propensity to form extended superlattics, such as that in the Figure. magnified image
Expression, secretion, and processing of staphylococcal nuclease by Corynebacterium glutamicum (1992)

The gene for staphylococcal nuclease (SNase), an extracellular enzyme of Staphylococcus aureus, was introduced into Corynebacterium glutamicum. The heterologous gene was expressed in this host organism, and SNase was efficiently exported to the culture medium. Amino-terminal sequencing of SNase secreted by C. glutamicum revealed that the signal peptide was apparently cleaved off at precisely the same position as in the original host, S. aureus. As with S. aureus, a second smaller form of SNase (A form), whose appearance is presumably the result of a secondary processing step, was found in the culture medium of the recombinant C. glutamicum strain. The A form was one residue shorter than the mature nuclease A produced by S. aureus. Variation of the sodium chloride concentration in the growth medium had a marked influence on the location and the processing of SNase by C. glutamicum. In a complex growth medium containing 4% sodium chloride, SNase was exclusively located in the supernatant, but a significant amount of the enzyme remained cell associated if the strain was grown in a low-salt medium. Also, high salt concentrations seemed to inhibit processing of the high-molecular-weight form of SNase (B form) to the smaller A form. Similarities and differences in the export and modes of processing of SNase by three different, nonrelated gram-positive host organisms are discussed. Finally, a versatile Escherichia coli-C. glutamicum tac-lacIq expression shuttle vector was constructed. With this vector, it was possible to achieve isopropyl-beta-D-galactopyranoside (IPTG)-inducible overexpression and secretion of SNase in C. glutamicum, whereby the expression level was dependent on the concentration of the inducer.
Germ-Line Transformation Involving DNA from theperiodLocus inDrosophila melanogaster: Overlapping Genomic Fragments that Restore Circadian and Ultradian Rhythmicity toper0andper−Mutants (1986)

P-element-mediated transformations involving DNA fragments from the period (per) clock gene of Drosophila melanogaster have shown that several subsegments of the locus restore rhythmicity to per0 or per- mutants. Such fragments overlap in a genomic region complementary to one transcript, a 4.5-kb RNA which is probably the per message, in that it is necessary and (in terms of expression from this X-chromosomal locus) sufficient for the fly's circadian rhythms. It is also at least necessary for the high-frequency oscillations normally produced by courting males as they vibrate their wings. The entirety of the 4.5-kb transcript is not necessary for rather strong rhythmicity; nor does it seem to be sufficient, in transformants, for wild-type behavioral phenotypes. A 0.9-kb RNA, homologous to genomic region immediately adjacent to the source of the 4.5-kb species, oscillates in its abundance over the course of a day; but coverage of this transcript source in several transformants carrying a per0 mutation--which eliminates the 0.9-kb RNA's oscillation--does not restore rhythmicity. All of the independently isolated arrhythmic mutations tested were covered by the same array of overlapping per+-derived DNA fragments, implying that the only portion of the locus which has mutated to arrhythmicity is complementary to the 4.5-kb transcript.