gebhart/patrepeval huggingface dataset:
Unequal distribution of N6-methyladenosine in influenza virus mRNAs. (1987)

Influenza virus mRNA is posttranscriptionally methylated at internal adenosine residues to form N6-methyladenosine (m6A). It has been previously shown that there is an average of three m6A residues per influenza virus mRNA (R. M. Krug, M. A. Morgan, and A. J. Shatkin, J. Virol. 20:45-53, 1976). To determine the distribution of m6A in the different influenza virus mRNAs, we purified six of the mRNAs by hybrid selection, digested them with nuclease, and determined their methylation patterns by high-pressure liquid chromatography. The amount of m6A in the different mRNAs varied from one in matrix to eight in hemagglutinin.
Wide tuning range wavelength-swept laser with two semiconductor optical amplifiers (2005)

We demonstrate a wide tuning range high-speed wavelength-swept semiconductor laser based on a polygon scanning filter that is common to two laser cavities. Linear wavelength tuning was achieved over 145 nm around 1310 nm at a tuning repetition rate of 20 kHz. The wavelength tuning filter is expandable to accommodate multiple semiconductor optical amplifiers for further widening of the laser wavelength tuning range.
Natural history of multiple sclerosis: a unifying concept (2006)

Multiple sclerosis can follow very different patterns of evolution and variable rates of disability accumulation. This raises the issue whether it represents one or several distinct diseases. We assessed demographic and clinical characteristics in 1844 patients with multiple sclerosis that we categorized according to the classification of Lublin and Reingold (1996) into 1066 (58%) relapsing-remitting, 496 (27%) secondary progressive, 109 (6%) progressive relapsing and 173 (9%) primary progressive cases of multiple sclerosis. Relapsing-remitting and secondary progressive cases shared similar age at disease onset (median = 28.7 versus 29.5 years; P = 0.21), initial symptoms of the relapsing-remitting phase, degree of recovery from the first neurological episode, and time from the first to the second episode. By contrast, disease duration was twice as long in secondary progressive than in relapsing-remitting cases (mean +/- SD = 17.6 +/- 9.6 versus 8.7 +/- 8.6 years; P < 0.001). Progressive relapsing and primary progressive cases were essentially similar in their clinical characteristics. In patients experiencing a progressive course, median age at onset of progressive phase was similar in secondary progressive cases and in cases who were progressive from onset (39.1 versus 40.1 years; P = 0.47). The proportion of cases with superimposed relapses during progression was approximately 40% in both categories. Finally, the 1562 patients with an exacerbating-remitting initial course and the 282 patients with a progressive initial course of the disease were essentially similar with respect to the time course of disability accumulation from assignment to a given disability score, and the age at assignment of disability landmarks. These observational data suggest that the clinical phenotype and course of multiple sclerosis are age dependent. Relapsing-remitting disease can be regarded as multiple sclerosis in which insufficient time has elapsed for the conversion to secondary progression; secondary progressive forms as relapsing-remitting multiple sclerosis that has 'grown older'; and progressive from onset cases as multiple sclerosis 'amputated' from the usual preceding relapsing-remitting phase. Times to reach disability milestones, and ages at which these landmarks are reached, follow a predefined schedule not obviously influenced by relapses, whenever they may occur, or by the initial course of the disease, whatever its phenotype. This leads to a unifying concept of the disease in which primary and secondary progression might be regarded as essentially similar. From the clinical and statistical positions, multiple sclerosis might be considered as one disease with different clinical phenotypes rather than an entity encompassing several distinct diseases-the position of complexity rather than true heterogeneity.
Potential tumor biomarkers identified in ovarian cyst fluid by quantitative proteomic analysis, iTRAQ (2013)

Fluid from ovarian cysts connected directly to the primary tumor harbor many possible new tumor-specific biomarkers. We have identified 87 differentially expressed proteins and validated two candidates to verify the iTRAQ method. However several of the proteins are of interest for validation in a larger setting.
"Diffraction" and microscopy in solids and liquids by NMR (1975)

A new approach to the study of structure in solids and liquids by pulsed NMR is described. Either multiple-pulse line-narrowing sequences or single pulses, together with an applied linear magnetic field gradient are used. The theoretical analysis highlights the analogy with plane-wave scattering in optics and is illustrated experimentally with examples of diffraction by ordered and disordered systems and image formation or microscopy. The factors affecting the resolution of the technique are discussed, and the problems of reconstructing micrographs from their projections considered.
Determination of cytokine co‐expression in individual splenic CD4+ and CD8+ T cells from influenza virus‐immune mice (1998)

We have studied the patterns of interleukin-2 (IL-2), IL-4 and interferon-gamma (IFN-gamma) co-expression displayed by individual splenic CD4+ and CD8+ T cells in response to influenza virus immunization. Unseparated spleen cells obtained from mice intraperitoneally (i.p.) injected with A/PR8 (H1N1) influenza virus (PR8) were cultured for 24 hr in the presence of ultraviolet-inactivated PR8. As controls, cultures of both naive spleen cells stimulated with PR8 or of immune cells lacking the inactivated virus were used. The frequencies of CD4+ and CD8+ T cells expressing IL-2, IL-4 and IFN-gamma were determined by three-colour flow cytometric analysis of fixed and saponin-permeabilized cells fluorescent-stained for either CD4 or CD8 surface molecules and for one of the following combinations of two intracellular cytokines: IL-2/IL-4, IL-2/IFN-gamma and IL-4/IFN-gamma. The results showed that immunization with influenza virus induces in both CD4+ and CD8+ T cells a heterogeneity of cytokine response patterns that do not follow the type 1/type 2 polarized response model, but with substantial differences between the two populations. In fact, the analysis of the phenotypes of virus-immune CD8+ T cells revealed similar significant proportions of cells either expressing any one of the three cytokines or co-expressing combinations of them (i.e. IL-4/IL-2, IL-4/IFN-gamma and IL-2/IFN-gamma), whereas immune CD4+ T cells were seen to express almost exclusively a single cytokine per cell. The observed patterns of cytokine production suggest that influenza virus immunization induces the expression of a type 0 cytokine pattern at both population and single cell levels in CD8+ T cells and exclusively at the population level in CD4+ T cells.
The Crossover Sign Overestimates Acetabular Retroversion (2012)

A crossover sign is frequently present on well-positioned AP pelvis radiographs in the absence of acetabular retroversion. Variable AIIS morphology may explain the appearance of this sign in the presence or absence of acetabular retroversion.
The Uses of Argument (2003)

A central theme throughout the impressive series of philosophical books and articles Stephen Toulmin has published since 1948 is the way in which assertions and opinions concerning all sorts of topics, brought up in everyday life or in academic research, can be rationally justified. Is there one universal system of norms, by which all sorts of arguments in all sorts of fields must be judged, or must each sort of argument be judged according to its own norms? In The Uses of Argument (1958) Toulmin sets out his views on these questions for the first time. In spite of initial criticisms from logicians and fellow philosophers, The Uses of Argument has been an enduring source of inspiration and discussion to students of argumentation from all kinds of disciplinary background for more than forty years.
Chemically synthesized FePt nanoparticle material for ultrahigh-density recording (2005)

We have examined the magnetic anisotropy of the "heat-treated FePt nanoparticles" annealed in a magnetic field. The magnetic easy axis of the "heat-treated FePt nanoparticles" is found to be three-dimensional (3-D) random and a partial ordering fct structure is observed before annealing in the presence of a magnetic field. The value of M/sub r//M/sub s/ obtained is 0.5. After annealing in the presence of a magnetic field, the M-H loop indicates that the easy axis is oriented preferably in the perpendicular direction than along the in-plane direction. The value of H/sub c/(//)/H/sub c/(/spl perp/) at 10 K is 0.62 (1410 Oe/2250 Oe). The value of M/sub r//M/sub s/(/spl perp/) is 0.58 at 10 K larger than the value of M/sub r//M/sub s/(//). Therefore, a weak magnetic easy axis orientation is fundamentally possible on the chemically synthesized FePt nanoparticles. We have studied the recording characteristics of a 3-D random nanoparticle medium using a GUZIK spinstand and observed the recorded patterns for the medium by imaging with a magnetic force microscopy.
Apoptotic Cells Induce NF-κB and Inflammasome Negative Signaling (2015)

As they undergo phagocytosis, most early apoptotic cells negatively regulate proinflammatory signaling and were suggested as a major mechanism in the resolution of inflammation. The dextran sulfate sodium model is generally viewed as an epithelial damage model suited to investigate innate immune responses. Macrophages primed with LPS and subsequently exposed to DSS secrete high levels of IL-1β in an NLRP3-, ASC-, and caspase-1-dependent manner. The aim of this research was to test the therapeutic effect of a single dose of apoptotic cells in a DSS-colitis model and to explore possible mechanisms. Primary peritoneal macrophages, the DSS mice model, and Nlrp3-deficient mice, were used to assess the effect apoptotic cells on colitis. Immunohistochemistry, flow-cytometer, and western blots helped to explore the effect and mechanisms. Using a variety of NLRP3 triggering mechanisms, we show that apoptotic cells negatively regulate NF-κB and NLRP3 activation in primary peritoneal macrophages, at pre- and post-transcription levels, via inhibition of reactive oxygen species, lysosomal stabilization, and blocking K+ efflux. This property of apoptotic cells is demonstrated in a dramatic clinical, histological, and immunological amelioration of DSS colitis in Balb/c and B6 mice following a single administration of apoptotic cells.
Immunogenicity of wild and attenuated varicella‐zoster virus strains in rhesus monkeys (1984)

Thirty susceptible rhesus monkeys were inoculated with cell-free varicella-zoster virus strain OKA or strain KMcC. Both wild and attenuated strains were used. No clinical signs characteristic of human varicella were seen in any of the animals. Virus was not isolated from throat swabs, blood, or cerebrospinal fluid. Antibodies were measured by an enhanced plaque neutralization test. The wild and attenuated OKA strains produced comparable levels of antibodies for 3 months after inoculation. Attenuated KMcC strains produced lower titers than the wild strain. On rechallenge 3 months after primary inoculation animals boostered with the attenuated OKA strain developed significantly higher antibody titers than animals receiving the wild strain. Animals primed and challenged with the attenuated KMcC strains showed significantly lower antibody titers than animals which received the wild strain. The results indicate that the immunogenicity of attenuated OKA and KMcC strains in rhesus monkeys parallels the experience obtained with these strains in humans.
Origin of the scattering peak in microemulsions (1987)

From a Landau theory the static scattering intensity distribution I(q) of microemulsions is obtained. As essential ingredient we have included a negative gradient term in the free energy expression. The form of I(q)∼(a2+c1q2+c2q4)−1 yields for a2&amp;gt;0, c1&amp;lt;0, and c2&amp;gt;0 a single broad scattering peak and a q−4 decay at large q, both properties experimentally observed for a variety of microemulsions containing comparable amounts of water and oil. The peak originates from the modulation in the corresponding space correlation function given by γ(r)=(d/2πr)⋅e−r/ξ⋅sin(2πr/d). It is shown that the scattering intensity relation describes experimental literature data remarkably well, using only three fit parameters.
Characterization of polyhormonal insulin-producing cells derived in vitro from human embryonic stem cells (2013)

Human embryonic stem cells (hESCs) were used as a model system of human pancreas development to study characteristics of the polyhormonal cells that arise during fetal pancreas development. HESCs were differentiated into fetal-like pancreatic cells in vitro using a 33-day, 7-stage protocol. Cultures were ~90-95% PDX1-positive by day (d) 11 and 70-75% NKX6.1-positive by d17. Polyhormonal cells were scattered at d17, but developed into islet-like clusters that expressed key transcription factors by d33. Human C-peptide and glucagon secretion were first detected at d17 and increased thereafter in parallel with INS and GCG transcript levels. HESC-derived cells were responsive to KCl and arginine, but not glucose in perifusion studies. Compared to adult human islets, hESC-derived cells expressed ~10-fold higher levels of glucose transporter 1 (GLUT1) mRNA, but similar levels of glucokinase (GCK). In situ hybridization confirmed the presence of GLUT1 transcript within endocrine cells. However, GLUT1 protein was excluded from this population and was instead observed predominantly in non-endocrine cells, whereas GCK was co-expressed in insulin-positive cells. In rubidium efflux assays, hESC-derived cells displayed mild potassium channel activity, but no responsiveness to glucose, metabolic inhibitors or glibenclamide. Western blotting experiments revealed that the higher molecular weight SUR1 band was absent in hESC-derived cells, suggesting a lack of functional KATP channels at the cell surface. In addition, KATP channel subunit transcript levels were not at a 1:1 ratio, as would be expected (SUR1 levels were ~5-fold lower than KIR6.2). Various ratios of SUR1:KIR6.2 plasmids were transfected into COSM6 cells and rubidium efflux was found to be particularly sensitive to a reduction in SUR1. These data suggest that an impaired ratio of SUR1:KIR6.2 may contribute to the observed KATP channel defects in hESC-derived islet endocrine cells, and along with lack of GLUT1, may explain the absence of glucose-stimulated insulin secretion.
Mutation analysis of NTRK2 and NTRK3, encoding 2 tyrosine kinase receptors, in sporadic human medullary thyroid carcinoma reveals novel sequence variants (2001)

Somatic mutations in the proto-oncogene RET are found in 25% to 80% of sporadic medullary thyroid carcinomas (MTCs). The significance of somatic RET mutation in MTC initiation and progression, however, remains unknown. Like RET, TRK is a neurotrophic receptor tyrosine kinase. Immunostaining has shown that only a subset of normal C cells expresses Trk family receptors, but in C-cell hyperplasia, they consistently express NTRK2, with variable expression of NTRK1 and NTRK3. In later stages of MTC, NTRK2 expression was reduced while NTRK3 expression was increased. In the context of these data, we sought to determine whether sequence variants in NTRK2 and NTRK3 are responsible for these differences in protein expression. We determined the genomic structure of NTRK2 and found that it consists of at least 17 exons varying in size from 36 to 306 bp. Mutation analysis of sporadic MTC did not reveal any sequence variants in NTRK2 but did reveal 3 variants in NTRK3, c.573C>T (N191N, exon 5), c.678T>C (N226N, exon 6) and c.1488C>G (A496A, exon 12) occurring among 19 chromosomes (31%), 1 chromosome (2%) and 24 chromosomes (39%), respectively. Corresponding germline also harbored these variants. There was a trend toward excess association of the NTRK3 variant c.1488C>G (A496A) in cases (24/62 chromosomes, 39%) compared to controls (18/62, 29%), but this difference did not reach significance (p > 0.05). The remaining 2 NTRK3 variants occurred with similar frequencies between MTC cases and population-matched controls (19 vs. 17 and 1 vs. 0, p > 0.05). We conclude that sequence variants in NTRK2 and NTRK3 are not likely to be responsible for large differences in expression at the protein level, but we cannot exclude very low penetrance effects. © 2001 Wiley-Liss, Inc.
Efficient Computation of PageRank (1999)

Abstract This paper discusses efficient techniques for computing PageRank, a ranking met-ric for hypertext documents. We show that PageRank can be computed for very large subgraphs of the web (up to hundreds of millions of nodes) on machineswith limited main memory. Running-time measurements on various memory configurations are presented for PageRank computation over the 24-million-pageStanford WebBase archive. We discuss several methods for analyzing the convergence of PageRank based on the induced ordering of the pages. We presentconvergence results helpful for determining the number of iterations necessary to achieve a useful PageRank assignment, both in the absence and presence ofsearch queries.
SR proteins: a conserved family of pre-mRNA splicing factors. (1992)

We demonstrate that four different proteins from calf thymus are able to restore splicing in the same splicing-deficient extract using several different pre-mRNA substrates. These proteins are members of a conserved family of proteins recognized by a monoclonal antibody that binds to active sites of RNA polymerase II transcription. We purified this family of nuclear phosphoproteins to apparent homogeneity by two salt precipitations. The family, called SR proteins for their serine- and arginine-rich carboxy-terminal domains, consists of at least five different proteins with molecular masses of 20, 30, 40, 55, and 75 kD. Microsequencing revealed that they are related but not identical. In four of the family members a repeated protein sequence that encompasses an RNA recognition motif was observed. We discuss the potential role of this highly conserved, functionally related set of proteins in pre-mRNA splicing.
Expression pattern of fatty acid-binding proteins in human normal and cancer prostate cells and tissues. (2001)

We propose that there is a distinct balance between these groups of FABPs, whose altered regulation in cells may play a role in prostate cancer. Furthermore, the pattern of expression and secretion of FABPs have the potential to serve as a diagnostic marker for an aggressive phenotype of prostate cancer.
Paradoxical interactions between human delta hepatitis agent RNA and the cellular protein kinase PKR (1996)

The genome of the human delta hepatitis agent is a circular, highly structured single-stranded RNA lacking regular runs of RNA-RNA duplex longer than 15 bp. We have tested the ability of delta agent RNA to participate in reactions with a protein containing a motif which confers the ability to bind double-stranded RNA (dsRNA). Surprisingly, highly purified delta agent RNA preparations from which all traces of contaminating dsRNA have been removed activate PKR, the dsRNA-dependent protein kinase activity of mammalian cells (also known as DAI, P1-eIF-2, and p68 kinase). This behavior is in marked contrast to the interaction of PKR with a number of other highly structured viral single-stranded RNAs, which inhibit, rather than stimulate, activation of this kinase. PKR activation leads to inhibition of protein synthesis in the rabbit reticulocyte lysate system. Paradoxically, delta RNA failed to elicit the expected PKR-mediated inhibition of cell-free translation. Instead, delta RNA interfered with PKR activation and the translational block induced by dsRNA. We conclude that the interaction of PKR and delta agent RNA may represent a new category of protein-RNA interactions involving the dsRNA binding motif.
Purification and characterization of β-N-acetylhexosaminidase I2 from human liver (1986)

beta-N-Acetylhexosaminidase I2 was purified from human liver by a combination of concanavalin A chromatography, DEAE-cellulose chromatography, gel filtration and affinity chromatography on 2-acetamido-N-(6-aminohexanoyl)-2-deoxy-beta-D-glucopyranosylamine coupled to CNBr-activated Sepharose 4B. Its specific activity was 130 mumol/min per mg of protein compared with values of 150 and 320 mumol/min/mg of protein for beta-N-acetylhexosaminidases A and B purified from the same tissue. Km values for I2, A and B were 1.0 mM, 0.8 mM and 0.74 mM respectively. On gradient gel electrophoresis under non-denaturing conditions, hexosaminidase I2 behaved similarly to A and appeared to have an Mr between 100 000 and 110 000. beta-N-Acetylhexosaminidase I2 was resolved into two major polypeptides, of Mr 56 000 and 29 000, on SDS/polyacrylamide-gel electrophoresis under denaturing conditions. Immunoblotting with anti-(hexosaminidase alpha-subunit) serum confirmed that the 56 000-Mr component was the alpha-subunit and anti-(hexosaminidase B) serum reacted with the 29 000 Mr component. beta-N-Acetylhexosaminidase I2 more closely resembles form A than B, but the features of its structure that allow it to be separated from A on the basis of net charge have not yet been found.
Cloning and Characterization of a Novel Chromosomal Drug Efflux Gene in Staphylococcus aureus. (2002)

A novel drug efflux gene (named sepA, staphylococcal efflux pump gene) is cloned from antiseptic-resistant mutants of Staphylococcus aureus into Escherichia coli. The sepA gene conferred the reduction of susceptibility to acriflavine and the acceleration of ethidium bromide efflux from the E. coli cells. The sepA (474 bp) encoded the protein that has four predicted transmembrane segments. These results indicate that sepA gene is a multidrug-resistant gene and encodes a drug efflux protein.
A 900-MHz RF front-end with integrated discrete-time filtering (1996)

Discrete-time analog filters, rather than off-chip components, have been used to perform frequency selection and down conversion in the integrated front-end for a 900-MHz RF receiver. The first stage of frequency down conversion is implemented with a subsampling switched-capacitor sample-and-hold circuit clocked at 78 MHz. Subsequent stages of discrete-time filtering are realized using switched-capacitor biquadratic filters. An experimental prototype of the front-end had been integrated in a 0.6-/spl mu/m BiCMOS technology. The circuit provides a system gain of 36 dB and 32 dB suppression of interfering channels over a 40 MHz bandwidth. Referred to the system input, the third-order intercept-point is -16 dBm, and the spot input-referred noise is -82 dBm over a 30 kHz bandwidth. The experimental circuit dissipates 90 mW from a 3.3-V supply and occupies an active area of 1.9/spl times/1.9 mm/sup 2/.