gebhart/patrepeval huggingface dataset:
Expression of the SLAM Family of Receptors Adapter EAT-2 as a Novel Strategy for Enhancing Beneficial Immune Responses to Vaccine Antigens (2010)

Recent studies have shown that activation of the signaling lymphocytic activation molecule (SLAM) family of receptors plays an important role in several aspects of immune regulation. However, translation of this knowledge into a useful clinical application has not been undertaken. One important area where SLAM-mediated immune regulation may have keen importance is in the field of vaccinology. Because SLAM signaling plays such a critical role in the innate and adaptive immunity, we endeavored to develop a strategy to improve the efficacy of vaccines by incorporation of proteins known to be important in SLAM-mediated signaling. In this study, we hypothesized that coexpression of the SLAM adapter EWS-FLI1-activated transcript 2 (EAT-2) along with a pathogen-derived Ag would facilitate induction of beneficial innate immune responses, resulting in improved induction of Ag-specific adaptive immune responses. To test this hypothesis, we used rAd5 vector-based vaccines expressing murine EAT-2, or the HIV-1-derived Ag Gag. Compared with appropriate controls, rAd5 vectors expressing EAT-2 facilitated bystander activation of NK, NKT, B, and T cells early after their administration into animals. EAT-2 overexpression also augments the expression of APC (macrophages and dendritic cells) surface markers. Indeed, this multitiered activation of the innate immune system by vaccine-mediated EAT-2 expression enhanced the induction of Ag-specific cellular immune responses. Because both mice and humans express highly conserved EAT-2 adapters, our results suggest that human vaccination strategies that specifically facilitate SLAM signaling may improve vaccine potency when targeting HIV Ags specifically, as well as numerous other vaccine targets in general.
A Novel Mechanism for the Inhibition of Hyaluronan Biosynthesis by 4-Methylumbelliferone (2004)

Specific inhibitors of hyaluronan (HA) biosynthesis can be valuable therapeutic agents to prevent cancer invasion and metastasis. We have found previously that 4-methylumbelliferone (MU) inhibits HA synthesis in human skin fibroblasts and in group C Streptococcus. In this paper, the inhibition mechanism in mammalian cells was investigated using rat 3Y1 fibroblasts stably expressing HA synthase (HAS) 2. Exposure of the transfectants to the inhibitor resulted in significant reduction of HA biosynthesis and matrix formation. The evaluation of HAS transcripts and analysis of cell-free HA synthesis demonstrated the post-transcriptional suppression of HAS activity by MU. Most interesting, the post-transcriptional suppression of HAS activity was also observed using p-nitrophenol, a well known substrate for UDP-glucuronyltransferases (UGT). We investigated whether the inhibition was exerted by the glucuronidation of MU using both high pressure liquid chromatography and TLC analyses. The production of MU-glucuronic acid (GlcUA) was consistent with the inhibition of HA synthesis in HAS transfectants. MU-GlcUA was also detected at a similar level in control cells, suggesting that the glucuronidation was mediated by an endogenous UGT. Elevated levels of UGT significantly enhanced the inhibitory effects of MU. In contrast, the inhibition by MU was diminished to the control level when an excess of UDP-GlcUA was added to the cell-free HA synthesis system. We propose a novel mechanism for the MU-mediated inhibition of HA synthesis involving the glucuronidation of MU by endogenous UGT resulting in a depletion of UDP-GlcUA.
An 86-probe-set gene-expression signature predicts survival in cytogenetically normal acute myeloid leukemia (2008)

Patients with cytogenetically normal acute myeloid leukemia (CN-AML) show heterogeneous treatment outcomes. We used gene-expression profiling to develop a gene signature that predicts overall survival (OS) in CN-AML. Based on data from 163 patients treated in the German AMLCG 1999 trial and analyzed on oligonucleotide microarrays, we used supervised principal component analysis to identify 86 probe sets (representing 66 different genes), which correlated with OS, and defined a prognostic score based on this signature. When applied to an independent cohort of 79 CN-AML patients, this continuous score remained a significant predictor for OS (hazard ratio [HR], 1.85; P = .002), event-free survival (HR = 1.73; P = .001), and relapse-free survival (HR = 1.76; P = .025). It kept its prognostic value in multivariate analyses adjusting for age, FLT3 ITD, and NPM1 status. In a validation cohort of 64 CN-AML patients treated on CALGB study 9621, the score also predicted OS (HR = 4.11; P < .001), event-free survival (HR = 2.90; P < .001), and relapse-free survival (HR = 3.14, P < .001) and retained its significance in a multivariate model for OS. In summary, we present a novel gene-expression signature that offers additional prognostic information for patients with CN-AML.
Long-term changes in sciatic-evoked A-fiber dorsal horn field potentials accompany loose ligation of the sciatic nerve in rats (2000)

The goal of the present study was to examine whether loose ligation of the sciatic nerve was associated with long-term changes in neuronal excitability in the spinal dorsal horn in urethane-anesthetized rats. The sciatic nerve was stimulated with 0. 1 ms long pulses at 1 stimulus/5 min, and the evoked dorsal horn field potentials remained stable in the absence of tetanic stimulation. In one set of control and ligated animals, high-frequency tetanic stimulation was applied to the nerve at 50 Hz (one 400 ms train of twenty 0.1 ms pulses), and the field potentials were recorded again (1 stimulus/5 min) for up to 4 h post-tetanus. In control animals, this protocol produced significant increases in field potential amplitudes at 15, 30 and 60 min post-tetanus. Interestingly, after this time the evoked field potentials began to decrease, and attained less than 50% of their pre-tetanic values at 240 min post-tetanus. In contrast, in ligated rats the pattern of post-tetanic potentiation was significantly different as the increases in amplitude persisted, and at 240 min post-tetanus the field potentials were almost twice their baseline values. In another set of control and ligated animals, low-frequency tetanic stimulation was applied at 5 Hz (one 400 ms train of two 0.1 ms pulses). Again a differential pattern of post-tetanic responses between control and ligated rats was seen. In control animals, a significant decrease in amplitude was evident within 30 min, and the depression became progressively more pronounced as the field potentials attained about a quarter of their baseline values at 180 min, and remained at these low levels at 240 min post-tetanus. On the other hand, in ligated animals, the depression was not significant, and at 240 min post-tetanus the field potentials were still at about 80% of their baseline values. These data demonstrate that long-term changes in spinal dorsal horn neuronal excitability accompany sciatic ligation to perhaps contribute to the development of neuropathic pain. These changes may result from a lessening of normally strong inhibitory processes in the spinal dorsal horn to generate conditions which favor post-tetanic potentiation over depression of dorsal horn neuronal responses.
Phase variation in pneumococcal opacity: relationship between colonial morphology and nasopharyngeal colonization (1994)

When colonies of encapsulated isolates of Streptococcus pneumoniae are viewed with oblique, transmitted light on a transparent surface, they are heterogeneous in appearance because of variation in opacity. There is spontaneous phase variation among at least three discernible phenotypes at frequencies from 10(-3) to 10(-6). The ability to detect differences in opacity varies according to serotype, but variation is independent of capsule expression. Electron microscopy shows no difference in chain length but suggests that autolysis occurs earlier in the growth of the transparent variant. There was no identifiable difference in membrane protein profiles of opaque and transparent variants of the same strain. In an infant rat model of nasopharyngeal carriage, there was no significant colonization by opaque variants. Efficient and stable colonization by the transparent variants was observed, suggesting a selective advantage for this phenotype in the nasopharynx. In contrast, there was no difference in the incidence of bacteremia or in the 50% lethal dose among the variants following their intraperitoneal inoculation. These results suggest that phase variation which is marked by differences in colonial morphology may provide insight into the interaction of the pneumococcus with its host.
In Vitro and In Vivo Activities of Novel 6-Methylidene Penems as β-Lactamase Inhibitors (2004)

Novel penem molecules with heterocycle substitutions at the 6 position via a methylidene linkage were investigated for their activities and efficacy as beta-lactamase inhibitors. The concentrations of these molecules that resulted in 50% inhibition of enzyme activity were 0.4 to 3.1 nM for the TEM-1 enzyme, 7.8 to 72 nM for Imi-1, 1.5 to 4.8 nM for AmpC, and 14 to 260 nM for a CcrA metalloenzyme. All the inhibitors were more stable than imipenem against hydrolysis by hog and human dehydropeptidases. Piperacillin was combined with a constant 4-microg/ml concentration of each inhibitor for MIC determinations. The combinations reduced piperacillin MICs by 2- to 32-fold for extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli and Klebsiella pneumoniae strains. The MICs for piperacillin-resistant (MIC of piperacillin, >64 microg/ml) strains of Enterobacter spp., Citrobacter spp., and Serratia spp. were reduced to the level of susceptibility (MIC of piperacillin, < or =16 microg/ml) when the drug was combined with 4, 2, or 1 microg of these penem inhibitors/ml. Protection against acute lethal bacterial infections with class A and C beta-lactamase- and ESBL-producing organisms in mice was also demonstrated with piperacillin plus inhibitor. Median effective doses were reduced by approximately two- to eightfold compared to those of piperacillin alone when the drug was combined with the various inhibitors at a 4:1 ratio. Pharmacokinetic analysis after intravenous administration of the various inhibitors showed mean residence times of 0.1 to 0.5 h, clearance rates of 15 to 81 ml/min/kg, and volumes of distribution between 0.4 and 2.5 liters/kg. The novel methylidene penem molecules inhibit both class A and class C enzymes and warrant further investigation for potential as therapeutic agents when used in combination with a beta-lactam antibiotic.
Reconstitution and Molecular Analysis of an Active Human Immunodeficiency Virus Type 1 Nef/p21-Activated Kinase 2 Complex (2005)

Human immunodeficiency virus type 1 (HIV-1) Nef activation of p21-activated kinase 2 (PAK-2) was recapitulated in a cell-free system consisting of in vitro-transcribed RNA, rabbit reticulocyte lysate, and microsomal membranes on the basis of the following observations: (i) Nef associated with a kinase endogenous to the rabbit reticulocyte lysate that was identified as PAK-2, (ii) Nef-associated kinase activity was detected with Nefs from HIV-1(SF2), HIV-1(YU2), and SIV(mac239), (iii) kinase activation was not detected with a myristoylation-defective Nef (HIV-1(SF2)NefG2A) or with a Nef defective in PAK-2 activation but fully competent in other Nef functions (HIV-1(SF2)NefF195I), and (iv) Nef-associated kinase activation required activated endogenous p21 GTPases (Rac1 or Cdc42). The cell-free system was used to analyze the mechanism of Nef activation of PAK-2. First, studies suggest that the p21 GTPases may act transiently to enhance Nef activation of PAK-2 in vitro. Second, addition of wortmannin to the cell-free system demonstrated that Nef activation of PAK-2 does not require PI 3-kinase activity. Third, ultracentrifugation analysis revealed that whereas the majority of Nef and PAK-2 partitioned to the supernatant, Nef-associated PAK-2 activity partitioned to the membrane-containing pellet as a low-abundance complex. Lastly, Nef activation of PAK-2 in vitro requires addition of microsomal membranes either during or after translation of the Nef RNA. These results are consistent with a model in which activation of PAK-2 by Nef occurs by recruiting PAK-2 to membranes. As demonstrated herein, the cell-free system is a new and important tool in the investigation of the mechanism of PAK-2 activation by Nef.
Reduction of proximity losses in coupled inductors (1991)

The paper presents an investigation into the leakage fields and eddy current losses in the windings of inductors and coupled inductors used in high frequency applications. It shows that the eddy current losses in the windings can be reduced significantly by the use of distributed airgaps, and that under these conditions the leakage fields are predominantly one dimensional so that the losses can be predicted analytically. Mutual losses produced by one winding in another are examined. It is shown how ferrite core designs can be modified to ameliorate further AC winding losses. These techniques taken together show that winding eddy current losses in inductors and coupled inductors can be reduced almost by an order of magnitude. Thus inductor efficiency can be improved, and the way becomes open for the design of inductors for higher frequency circuits.
Size constraints for targeting post‐transcriptional gene silencing and for RNA‐directed methylation in <i>Nicotiana benthamiana</i> using a potato virus X vector (2001)

Using a recombinant potato virus X (PVX) vector, we investigated the relationship between the length of RNA sequence identity with a transgene and the ability to promote post-transcriptional gene silencing (PTGS) and transgene methylation. The lower size limit required for targeting reporter transgene mRNA de novo using PTGS was 23 nucleotides (nt) of complete identity, a size corresponding to that of small RNAs associated with PTGS in plants and RNA interference (RNAi) in animals. The size and sequence specificity were also explored for PTGS-associated transgene methylation and for the targeting of the vector RNA. The PTGS-competent short sequences resulted in similar patterns of methylation. In all cases, including specific sequences of 33 nt with or without symmetrical cytosine residues, the methylation was distributed throughout the transcribed region of the transgene. In contrast, short sequences lacking symmetrical cytosines were less efficient at promoting PTGS of the transgene mRNA. Short gfp sequences in the PVX vector provided as effective a target for the degradation of viral RNA as was found for PVX carrying the complete gfp cDNA. Short sequences were able to initiate PTGS of an endogenous gene, phyotene desaturase, although this occurred in the absence of DNA methylation. This experimental approach provides important insights into the relationship between short RNA sequences and PTGS.
THE USE OF INTERNET AMONG MALAYSIAN LIBRARIANS (1998)

The Internet is fast becoming an important tool for librarians. The purpose of this study was to determine how librarians in Malaysia use the Internet for work-related purposes. A questionnaire was sent to 158 librarians, and 83 usable responses were received. The main findings indicated 90% of the respondents used the Internet for work-related purposes. The majority were recent users and had first learned to use it, from a friend or colleague, although they had also attended some formal training sessions. The users spent an average of 45.8 minutes per access, and averaged 6.97 hours per week on the net. All of them used the WWW, with the majority using it at least once a day, while 97.3% used the e-mail, 62.0% used Telnet, 31.5% used file transfers and 28.2% used newsgroups. A vast majority regarded the Internet as essential tool for librarians and felt that it had contributed to increased efficiency in their workplace. The main problem faced was the lack of time.
Antibody-Specific Model of Amino Acid Substitution for Immunological Inferences from Alignments of Antibody Sequences (2014)

Antibodies are glycoproteins produced by the immune system as a dynamically adaptive line of defense against invading pathogens. Very elegant and specific mutational mechanisms allow B lymphocytes to produce a large and diversified repertoire of antibodies, which is modified and enhanced throughout all adulthood. One of these mechanisms is somatic hypermutation, which stochastically mutates nucleotides in the antibody genes, forming new sequences with different properties and, eventually, higher affinity and selectivity to the pathogenic target. As somatic hypermutation involves fast mutation of antibody sequences, this process can be described using a Markov substitution model of molecular evolution. Here, using large sets of antibody sequences from mice and humans, we infer an empirical amino acid substitution model AB, which is specific to antibody sequences. Compared with existing general amino acid models, we show that the AB model provides significantly better description for the somatic evolution of mice and human antibody sequences, as demonstrated on large next generation sequencing (NGS) antibody data. General amino acid models are reflective of conservation at the protein level due to functional constraints, with most frequent amino acids exchanges taking place between residues with the same or similar physicochemical properties. In contrast, within the variable part of antibody sequences we observed an elevated frequency of exchanges between amino acids with distinct physicochemical properties. This is indicative of a sui generis mutational mechanism, specific to antibody somatic hypermutation. We illustrate this property of antibody sequences by a comparative analysis of the network modularity implied by the AB model and general amino acid substitution models. We recommend using the new model for computational studies of antibody sequence maturation, including inference of alignments and phylogenetic trees describing antibody somatic hypermutation in large NGS data sets. The AB model is implemented in the open-source software CodonPhyML (http://sourceforge.net/projects/codonphyml) and can be downloaded and supplied by the user to ProGraphMSA (http://sourceforge.net/projects/prographmsa) or other alignment and phylogeny reconstruction programs that allow for user-defined substitution models.
Analysis of <i>Toxoplasma gondii</i> stably transfected with a transmembrane variant of its major surface protein, SAG1 (1998)

We have genetically engineered Toxoplasma gondii so that its major surface antigen SAG1 is anchored by a human transmembrane domain (SAG1-TM) instead of its natural GPI anchor (SAG1-GPI) in order to initiate studies to address the function of this protein anchor in parasitic protozoa as well as to get insights into the functional role of SAG1. Our results show that SAG1-TM is correctly folded (at least as judged by the presence of conformationally dependent epitopes) and targeted to the surface of the parasite, indicating that the GPI anchor does not determine its localization nor overall three-dimensional structure. No significant difference was seen in any aspect of the growth of the SAG1-TM mutant. However, compared to the natural SAG1-GPI, SAG1-TM does not form strong associations with itself and/or other molecules in high molecular weight complexes suggesting that allowing such complexes to form may be one role of the GPI anchor. The in vitro half-life of SAG1-TM of extracellular parasites is significantly lower than that of SAG1-GPI suggesting a stabilizing function of the glycolipid anchor against degradation and/or membrane release. Antibodies to SAG1 are shed from SAG1-TM parasites as they invade, just as they are stripped from SAG1-GPI bearing parasites. The stripping, therefore, is unlikely to be driven by the action of lipases.
Localization of a tumor suppressor gene associated with progression of human prostate cancer within a 1.2 Mb region of 8p22‐p21.3 (1995)

Human prostate cancers frequently show loss of heterozygosity at loci on the short arm of chromosome 8. In order to take a step toward isolation of the putative tumor suppressor gene(s) on 8p via positional cloning, we performed high-resolution deletion mapping in 46 prostate cancers (stage B, 20 cases; stage C, 8 cases; endocrine therapy-resistant cancer death, 18 cases) using new 12 restriction fragment length polymorphism markers for this chromosomal region. Allelic losses were observed in 25 of the 44 cases (57%) that were informative with at least one locus. Detailed deletion mapping defined a 1.2 Mb commonly deleted region at 8p22-p21.3 flanked by markers cMSR-32 and C18-1051. A second region of common deletion was identified between C18-1312 and C18-494 at 8p21-8p11.22, suggesting that at least two tumor suppressor genes associated with prostate cancer are present on chromosome arm 8p. Allelic losses on 8p were observed more frequently in the cancer death cases (14/17, 82%) than in early-stage tumors (11/27, 40%; P < 0.01, Fisher's exact test). In two out of 7 patients for whom DNA was available from metastatic cancers as well as from normal tissues and primary tumors, the primary cancer foci had no detectable abnormality of 8p, but the metastatic tumors showed loss of heterozygosity. These results suggest that inactivation of tumor suppressor genes on 8p plays an important role in the progression of prostate cancer.
Iron in kaolinite: II. The relationship between kaolinite crystallinity and iron content (1980)

Abstract Calibration of the internal and external signals appearing at g eff ∼4 in the electron paramagnetic resonance (EPR) spectra of twenty-four kaolinites, has led to the recognition of two types of kaolinite-iron. The amount of iron associated with the internal signal (I iron) shows good inverse correlations with parameters used to describe the degree of crystalline perfection in kaolinite. Iron associated with the external signal (E iron) is insensitive to crystalline order. By considering both the amount and nature of the iron, the kaolinites investigated are placed in three groups. The first contains well-crystallized varieties characterized by low total iron and EPR spectra consisting mainly of an E signal. Poorly-crystallized kaolinites contain more iron and are characterized by a fifty-fifty partition of this iron into E and I sites. The third group contains samples which are intermediate with respect to both the amount and nature of the iron.
Channel capacity enhancement scheme for satellite communication system (2007)

In this paper, a hierarchical modulation scheme(and also known as embedded, multi-resolution, or asymmetrical constellation scheme) is studied for transmission of multimedia system. A hierarchical modulation scheme is presented to upgrade an existing digital broadcast system by adding more data stream in its transmissions. The hierarchical modulation is composed of a basic constellation, which is the same as in the original system, and a secondary constellation, which carries the additional data for the upgraded system. The upgraded system with the hierarchical modulation is backward compatible (BC mode) in the sense that receivers that have been deployed in the original system can continue receiving data in the basic constellation. Hierarchical receivers can be designed to receive data carried in the secondary constellation, as well as those in the basic constellation. Specifically, we propose general design guidelines for multimedia transmission over AWGN channels with an hierarchical Amplitude Phase Shift-Keying(APSK) constellation.