gebhart/patrepeval huggingface dataset:
Characterization of the glycosylation sites in yeast external invertase. I. N-linked oligosaccharide content of the individual sequons. (1988)

External invertase is the product of the SUC2 gene of Saccharomyces cerevisiae. The deduced sequence of this enzyme (Taussig, R., and Carlson, M. (1983) Nucleic Acid Res. 11, 1943-1954) reveals it to contain 14 potential N-linked glycosylation sites, or sequons, although only 9-10 appear to be glycosylated (Trimble, R. B., and Maley, F. (1977) J. Biol. Chem. 252, 4409-4412). To determine the location of the glycosylated sequons, external invertase was deglycosylated with endo-beta-acetylglucosaminidase H and its component peptides analyzed by both fast atom bombardment mass spectrometry (FABMS) and classical peptide isolation procedures. By use of the former technique most of the glucosamine-containing sequons could be located and by the latter sufficient amounts of small glucosamine-containing peptides were isolated to enable their quantitation. From the combined FABMS and glucosamine analyses, it was established that eight of the sequons in a subunit of invertase are either completely or almost completely glycosylated, while five others are glycosylated to the extent of about 50% or less. In the case of two overlapping sequons (4 and 5), which include Asn92-Asn93-Thr-Ser, only the first Asn was glycosylated. Thus, all but one of the sequons of external invertase are glycosylated to some extent, giving an appearance of only 9-10 N-linked oligosaccharides/subunit. The sequence identity of both external and internal invertase was verified by FABMS and by peptide sequence analysis. In only one site was an amino acid found to differ from that deduced from the DNA sequence of the SUC2 gene. This occurred at position 390 where a proline was found in place of alanine, which could result from a single base change in the triplet specifying the latter amino acid.
RETRACTED: Somatic hypermutation maintains antibody thermodynamic stability during affinity maturation (2013)

Somatic hypermutation and clonal selection lead to B cells expressing high-affinity antibodies. Here we show that somatic mutations not only play a critical role in antigen binding, they also affect the thermodynamic stability of the antibody molecule. Somatic mutations directly involved in antigen recognition by antibody 93F3, which binds a relatively small hapten, reduce the melting temperature compared with its germ-line precursor by up to 9 °C. The destabilizing effects of these mutations are compensated by additional somatic mutations located on surface loops distal to the antigen binding site. Similarly, somatic mutations enhance both the affinity and thermodynamic stability of antibody OKT3, which binds the large protein antigen CD3. Analysis of the crystal structures of 93F3 and OKT3 indicates that these somatic mutations modulate antibody stability primarily through the interface of the heavy and light chain variable domains. The historical view of antibody maturation has been that somatic hypermutation and subsequent clonal selection increase antigen-antibody specificity and binding energy. Our results suggest that this process also optimizes protein stability, and that many peripheral mutations that were considered to be neutral are required to offset deleterious effects of mutations that increase affinity. Thus, the immunological evolution of antibodies recapitulates on a much shorter timescale the natural evolution of enzymes in which function and thermodynamic stability are simultaneously enhanced through mutation and selection.
Frequency of herpes simplex virus-specific murine cytotoxic T lymphocyte precursors in mitogen- and antigen-driven primary in vitro T cell responses. (1987)

The aim of this study was to assess and to compare the frequencies and specificities of herpes simplex virus (HSV)-specific cytotoxic T lymphocyte precursors (CTL-p) in mitogen (concanavalin A)-activated splenic T cells, as well as in antigen-activated splenic T cells of normal nonimmunized mice. In the mitogen-driven system one of 130 T cell blasts developed clonal progenies able to lyse specifically HSV-infected syngeneic targets. In the antigen-driven system HSV-specific CTL-p could be detected in normal lymphocytes provided the stimulator cells used were enriched for dendritic cells and pulsed with high concentrations of heat-inactivated HSV. Depending on the mouse strain used, the frequencies of HSV-specific CTL-p ranged from 1/500 to 1/10,000 in normal mice. Upon antigen priming within local lymph node cells, an increase of frequencies from 1/500 to 1/170 was observed in CBA/Ca mice.
Nonlinear polymer-clad silicon slot waveguide modulator with a half wave voltage of 0.25V (2008)

We report on an electro-optic modulator fabricated from a silicon slot waveguide and clad in a nonlinear polymer. In this geometry, the electrodes form parts of the waveguide, and the modulator driving voltage drops across a 120nm slot. As a result, a half wave voltage of 0.25V is achieved near 1550nm. This is one of the lowest values for any modulator obtained to date. As the nonlinear polymers are extremely resistive, our device also has the advantage of drawing almost no current, suggesting this type of modulator could operate at exceedingly low power.
Molecular Characterization of the S-Adenosyl-l-methionine:3′-Hydroxy-N-methylcoclaurine 4′-O-Methyltransferase Involved in Isoquinoline Alkaloid Biosynthesis in Coptis japonica (2000)

S-adenosyl-L-methionine:3'-hydroxy-N-methylcoclaurine 4'-O-methyltransferase (4'-OMT) catalyzes the conversion of 3'-hydroxy-N-methylcoclaurine to reticuline, an important intermediate in synthesizing isoquinoline alkaloids. In an earlier step in the biosynthetic pathway to reticuline, another O-methyltransferase, S-adenosyl-L-methionine:norcoclaurine 6-O-methyltransferase (6-OMT), catalyzes methylation of the 6-hydroxyl group of norcoclaurine. We isolated two kinds of cDNA clones that correspond to the internal amino acid sequences of a 6-OMT/4'-OMT preparation from cultured Coptis japonica cells. Heterologously expressed proteins had 6-OMT or 4'-OMT activities, indicative that each cDNA encodes a different enzyme. 4'-OMT was purified using recombinant protein, and its enzymological properties were characterized. It had enzymological characteristics similar to those of 6-OMT; the active enzyme was the dimer of the subunit, no divalent cations were required for activity, and there was inhibition by Fe(2+), Cu(2+), Co(2+), Zn(2+), or Ni(2+), but none by the SH reagent. 4'-OMT clearly had different substrate specificity. It methylated (R,S)-6-O-methylnorlaudanosoline, as well as (R, S)-laudanosoline and (R,S)-norlaudanosoline. Laudanosoline, an N-methylated substrate, was a much better substrate for 4'-OMT than norlaudanosoline. 6-OMT methylated norlaudanosoline and laudanosoline equally. Further characterization of the substrate saturation and product inhibition kinetics indicated that 4'-OMT follows an ordered Bi Bi mechanism, whereas 6-OMT follows a Ping-Pong Bi Bi mechanism. The molecular evolution of these two related O-methyltransferases is discussed.
Genetic Control of Surface Curvature (2003)

Although curvature of biological surfaces has been considered from mathematical and biophysical perspectives, its molecular and developmental basis is unclear. We have studied the cin mutant of Antirrhinum, which has crinkly rather than flat leaves. Leaves of cin display excess growth in marginal regions, resulting in a gradual introduction of negative curvature during development. This reflects a change in the shape and the progression of a cell-cycle arrest front moving from the leaf tip toward the base. CIN encodes a TCP protein and is expressed downstream of the arrest front. We propose that CIN promotes zero curvature (flatness) by making cells more sensitive to an arrest signal, particularly in marginal regions.
Overexpression of Rat Heat Shock Protein 70 Reduces Neuronal Injury after Transient Focal Ischemia, Transient Global Ischemia, or Kainic Acid-induced Seizures (2003)

The results demonstrate that overexpression of hsp70 reduces neuronal injury after ischemia and seizures. The reduction in the number of terminal deoxynucleotidyl transferase-mediated biotinylated deoxyuridine triphosphate nick end-labeling-positive cells in hsp70 Tg mice suggests that hsp70 overexpression might reduce apoptotic cell death.
Promotion and Subsequent Inhibition of Plasminogen Activation after Administration of Intravenous Endotoxin to Normal Subjects (1989)

To evaluate the effect of endotoxin on the fibrinolytic response, we administered Escherichia coli endotoxin (4 ng per kilogram of body weight) intravenously to 19 healthy volunteers and measured fibrinolytic proteins, protease inhibitors, neutrophil elastase, and von Willebrand factor in serial blood samples obtained over 24 hours. One hour after endotoxin administration, the level of tissue plasminogen activator (t-PA) antigen rose from 10 to 23 ng per milliliter, peaking at 52 ng per milliliter at three hours. The level of alpha 2-plasmin inhibitor-plasmin complexes increased sevenfold, peaking at three hours. Plasminogen-activator inhibitor-1 activity rose more slowly, from 7 U per milliliter to a maximum of 49 U per milliliter at five hours. The concentrations of neutrophil elastase and von Willebrand antigen were unchanged at one hour, increased approximately threefold by 3 hours, and remained elevated at 24 hours. None of these measures changed in a control group (n = 5) given intravenous saline instead of endotoxin. We studied t-PA functional activity in four subjects. The level of activity rose rapidly, from 1.2 ng per milliliter at base line to 8.3 ng per milliliter at one hour and 13.9 ng per milliliter at two hours; it was undetectable at three hours. This increase in plasminogen activator activity was abolished in vitro by incubation of t-PA with an antiserum specific for human t-PA, suggesting that t-PA may be directly responsible for plasmin generation in the response to endotoxin. We conclude from this study of healthy subjects that endotoxin activates the fibrinolytic system, beginning with release of t-PA in the blood within one hour. The early activation of plasmin by endotoxin may prevent thrombosis, and the increase in fibrinolysis is then offset by the release of plasminogen activator inhibitor.
Interferon and TNF family soluble inflammatory mediators are detected prior to and increase at Systemic Lupus Erythematosus classification in serum samples from military personnel acquired from the Department of Defense Serum Repository (P3087) (2013)

Abstract Processes that lead to clinical illness in SLE years before diagnosis are not well characterized. This study evaluates the temporal relationship between autoantibody production, cytokine levels and the onset of SLE. Serial sera from 60 SLE cases before diagnosis with no ACR criteria to SLE classification (average timespan=4.4 years) and matched healthy controls (HC) were obtained from the DODSR. Sera samples were tested for autoantibodies (BioPlex2200), C-reactive protein (hs-CRP), Von Willebrand’s Factor (VWF) and 32 soluble inflammatory mediators, including cytokines, chemokines, and soluble receptors. Patient samples before ACR classification had significant (p &amp;lt; 0.01) alterations in 16 soluble mediators of inflammation, as well as VWF and hs-CRP. TNF Receptor levels, TNFRI, TNFRII, BLyS, and APRIL, dramatically increased as lupus classification approached (p &amp;lt; 0.001). The increase in TNFR shedding parallels the accumulation of autoantibodies in SLE cases. Interferon (IFN)-associated mediators of inflammation, IFN-γ, IP-10, MIG, and MIP-1α (p &amp;lt; 0.01), were also increased leading up to classification. That these alterations are present prior to the transition to active SLE suggests that multiple perturbations in immune-mediated inflammatory processes occur long before clinical classification and suggest that high-risk, pre-clinical individuals, can be identified before their illness is clinically manifested and damage occurs.
Metabolism of taxol by human hepatic microsomes and liver slices: participation of cytochrome P450 3A4 and an unknown P450 enzyme. (1994)

Incubation of taxol with human hepatic microsomal fractions or freshly isolated human liver slices yields three metabolite high performance liquid chromatography peaks, metabolite A, metabolite B, and 6 alpha-hydroxytaxol. These metabolites are formed in patients given taxol, with 6 alpha-hydroxytaxol formation representing the principal biotransformation pathway. Metabolite B and 6 alpha-hydroxytaxol are shown to be products of different, highly regioselective cytochrome P-450 (P450) enzymes, while metabolite A results from stepwise metabolism by each of these enzymes. Correlation of metabolite B formation with P450 3A markers was good (r2 = 0.91-0.94), but the correlation of 6 alpha-hydroxytaxol formation with markers for several P450 enzymes was poor. Chemical inhibitors that selectively inhibited metabolite B formation (troleandomycin, cyclosporine), that selectively inhibited 6 alpha-hydroxytaxol formation (naringenin, quercetin), or that nonselectively inhibited both pathways (felodipine, ketoconazole) were found. Metabolite B formation was selectively reduced by anti-P450 3A4 antibodies. Expressed human P450 3A4 preparations were efficient catalysts of metabolite B formation; no expressed P450 preparation tested showed a capacity for catalyzing taxane 6 alpha-hydroxylation reactions. The combined results of several experimental approaches show that P450 3A4 is the major catalyst of metabolite B formation and that the identity of the P450 enzyme or enzymes responsible for 6 alpha-hydroxytaxol formation cannot be assigned with certainty.
Biomarker discovery for colon cancer using a 761 gene RT-PCR assay (2007)

We have developed a high throughput, quantitatively precise multi-analyte gene expression platform for biomarker discovery that approaches low density DNA arrays in numbers of genes analyzed while maintaining the high specificity, sensitivity and reproducibility that are characteristics of RT-PCR. Biomarkers discovered using this approach can be transferred to a clinical reference laboratory setting without having to re-validate the assay on a second technology platform.
Preparation of Ni- or Pt-Containing Cyclic Esters by Oxidative Addition of Cyclic Carboxylic Anhydrides and Their Properties (1984)

Abstract Metal containing cyclic ester complexes, (Remark: Graphics omitted.)(L=1,2-bis(diphenylphosphino)ethane (dpe) or 2,2′-bipyridine (bpy); R1, R2=H or CH3) and (Remark: Graphics omitted.) (L=tricyclohexylphosphine (PCy3) or dpe; n=1 or 2), have been prepared by oxidative addition of cyclic carboxylic anhydrides to zero-valent metal complexes. These complexes have been characterized by elemental analysis and spectroscopies (IR as well as 1H-, 13C{1H}-, and 31P{1H}-NMR) and chemical reactivities. Rate of the oxidative addition of succinic anhydride to Ni(bpy)(cod) (cod=1,5-cyclooctadiene) is expressed by a second order rate equation, R=k[Ni(bpy)(cod)][succinic anhydride], and temperature dependence of k gives the activation energy of 68 kJ mol−1. The reaction of methylsuccinic anhydride with Ni(cod)2 in the presence of tertiary phosphine or bpy affords two isomers, (Remark: Graphics omitted.) and (Remark: Graphics omitted.), corresponding to two modes of C–O bond cleavage in methylsuccinic anhydride promoted by Ni; dependence of the ratio between the two isomers on the kind of ligand added and reaction conditions has been examined.
Antiparasitic Effects of the Intra-Golgi Transport Inhibitor Megalomicin (1998)

The macrolide antibiotic megalomicin (MGM) has been shown to inhibit vesicular transport between the medial- and trans-Golgi, resulting in the undersialylation of cellular proteins (P. Bonay, S. Munro, M. Fresno, and B. Alarcón, J. Biol. Chem. 271:3719-3726, 1996). Due to the effects of MGM on the Golgi and on the replication of enveloped viruses, we decided to test whether it has any antiparasitic activity. The results showed that MGM has potent activity against the epimastigote stage of Trypanosoma cruzi, producing a 50% inhibitory concentration (IC50) of 0.2 microg/ml. Furthermore, MGM was also active against the intracellular replicative, amastigote form of T. cruzi, completely preventing its replication in infected murine LLC/MK2 macrophages at a dose of 5 microg/ml. Although less potent, MGM was also active against Trypanosoma brucei epimastigotes (IC50, 2 microg/ml) and Leishmania donovani and Leishmania major promastigotes (IC50, 3 and 8 microg/ml, respectively). MGM also blocked intracellular replication of the asexual stage of Plasmodium falciparum-infected erythrocytes at 1 microg/ml. Finally, MGM was active in an in vivo model, resulting in the complete protection of BALB/c mice from death caused by acute T. brucei infection and significantly reducing the parasitemia. These results suggest that MGM is a potential drug for the treatment of veterinary and human parasitic diseases.
Performance capture from sparse multi-view video (2008)

This paper proposes a new marker-less approach to capturing human performances from multi-view video. Our algorithm can jointly reconstruct spatio-temporally coherent geometry, motion and textural surface appearance of actors that perform complex and rapid moves. Furthermore, since our algorithm is purely meshbased and makes as few as possible prior assumptions about the type of subject being tracked, it can even capture performances of people wearing wide apparel, such as a dancer wearing a skirt. To serve this purpose our method efficiently and effectively combines the power of surface- and volume-based shape deformation techniques with a new mesh-based analysis-through-synthesis framework. This framework extracts motion constraints from video and makes the laser-scan of the tracked subject mimic the recorded performance. Also small-scale time-varying shape detail is recovered by applying model-guided multi-view stereo to refine the model surface. Our method delivers captured performance data at high level of detail, is highly versatile, and is applicable to many complex types of scenes that could not be handled by alternative marker-based or marker-free recording techniques.
Transactivation of GATA-1 promoter with ETS1, ETS2 and ERGB/Hu-FLI-1 proteins: stabilization of the ETS1 protein binding on GATA-1 promoter sequences by monoclonal antibody. (1993)

Ets family proteins activate transcription via binding to the GGAA core sequence located in the promoter/enhancer elements of many cellular and viral genes. GATA-1 is an erythroid-specific transcription factor. The promoter of the chicken GATA-1 gene contains multiple ets binding sites (EBS), two of them are present in palindromic form. The GATA-1 promoter has been shown to be activated by the E26 virus. In this study, we have analysed whether the palidromic EBS of the chicken GATA-1 promoter is a target for binding and activation by members of the cellular ets gene family products. The results herein indicate that both EBS in the palindrome are required for DNA-binding because mutations in either site reduces the activity by at least 95%. Moreover, DNA binding of ETS1 to the EBS palindrome is dramatically stabilized in the presence of a specific monoclonal antibody whose epitope maps between amino acid positions 240-260. Although each of the single sites bind, the efficiency of binding is extremely low. Furthermore, for efficient binding the two sites must be in an inverted configuration because of the fact that the oligonucleotide containing the left and right EBS in the same orientation binds 10-fold less than the oligonucleotide containing the EBS palindrome. Additionally, we show that the transcription of a reporter gene (CAT) either linked to the GATA-1 EBS palindrome or GATA-1 promoter can be activated by cotransfection with ETS1, alternatively-spliced ETS1, ETS2 or ERGB/Hu-FLI-1 expression vectors.
Field-programmable gate-array-based investigation of the error floor of low-density parity check codes for magnetic recording channels (2005)

Good performance of iterative detection and decoding using low-density parity check (LDPC) codes has stimulated great interest in the data storage industry. One major concern in using LDPC codes in the read channel is their error floor, which is still an open question. To investigate the performance of LDPC codes in low bit-error rates (BER/spl sim/10/sup -10/), we developed a high-throughput fully reconfigurable simulator using a field programmable gate array. Using this simulator, we are able to observe the performance of LDPC codes at low BER within a reasonably short time (10/sup -10/ within 1.5 h). We show the evaluation results for two types of LDPC codes.
Synthesis and Hydrogenation of Bis(imino)pyridine Iron Imides (2006)

Treatment of the iron bis(dinitrogen) complex, (iPrPDI)Fe(N2)2 (iPrPDI = (2,6-iPr2C6H3N=CMe)2C5H3N), with a series of aryl azides resulted in loss of 3 equiv of N2 and formation of the corresponding four-coordinate iron imide compounds, (iPrPDI)Fe(NAr). These complexes, two of which (Ar = 2,6-iPr2-C6H3 and 2,4,6-Me3-C6H2) have been characterized by X-ray diffraction, are significantly distorted from planarity. The metrical parameters in combination with Mössbauer spectroscopic and SQUID magnetic data suggest an intermediate spin iron(III) center antiferromagnetically coupled to a ligand-centered radical. Nitrene group transfer has been accomplished by addition of 1 atm of CO, yielding aryl isocyanates, ArNCO, and (iPrPDI)Fe(CO)2. Hydrogenation of the more sterically hindered members of the series furnished free aniline and the previously reported iron dihydrogen complex. Catalytic aryl azide hydrogenation has also been achieved, and the observed relative rates are consistent with N-H bond formation as the rate-determining step in aniline formation.
Extracting principal diagnosis, co-morbidity and smoking status for asthma research: evaluation of a natural language processing system (2006)

We consider the results promising, given the complexity of the discharge summaries and the extraction tasks.
LITEWORP: A Lightweight Countermeasure for the Wormhole Attack in Multihop Wireless Networks (2005)

In multihop wireless systems, such as ad-hoc and sensor networks, the need for cooperation among nodes to relay each other's packets exposes them to a wide range of security attacks. A particularly devastating attack is known as the wormhole attack, where a malicious node records control and data traffic at one location and tunnels it to a colluding node, which replays it locally. This can have an adverse effect in route establishment by preventing nodes from discovering routes that are more than two hops away. In this paper, we present a lightweight countermeasure for the wormhole attack, called LITEWORP, which does not require specialized hardware. LITEWORP is particularly suitable for resource-constrained multihop wireless networks, such as sensor networks. Our solution allows detection of the wormhole, followed by isolation of the malicious nodes. Simulation results show that every wormhole is detected and isolated within a very short period of time over a large range of scenarios. The results also show that the fraction of packets lost due to the wormhole when LITEWORP is applied is negligible compared to the loss encountered when the method is not applied.