gebhart/patrepeval huggingface dataset:
Biochemical, Genetic, and Serological Characterization of Two Capsule Subtypes among Streptococcus pneumoniae Serotype 20 Strains (2012)

The bacterial pathogen Streptococcus pneumoniae expresses one of over 90 structurally distinct polysaccharide (PS) capsule serotypes. Prior PS structural analyses of the vaccine-associated serotype 20 do not agree with reports describing the genes that mediate capsule synthesis. Furthermore, using immunized human sera-based assays, serological differences were recently noted among strains typed as serotype 20. We examined the capsule structures of two serologically dissimilar serotype 20 strains, 20α and 20β, by extensive biochemical analysis. 20α PS was composed of the previously described serotype 20 hexasaccharide repeat unit, whereas the 20β PS was composed of a novel heptasaccharide repeat unit containing an extra branching α-glucose residue. Genetic analysis of the subtypes revealed that 20α may have arisen from a 20β progenitor following loss of function mutation to the glycosyltransferase gene whaF. Conventional serotyping methods using rabbit polyclonal or mouse monoclonal antibodies were unable to distinguish the subtypes. However, genetic analysis of multiple "serotype 20" clinical isolates revealed that all strains contain the 20β genotype. We propose naming bacteria that express the previously described 20α capsule structure 20A and bacteria that express the novel 20β capsule structure 20B, a new pneumococcal serotype.
A specific transmembrane domain of a coronavirus E1 glycoprotein is required for its retention in the Golgi region. (1987)

The E1 glycoprotein of the avian coronavirus infectious bronchitis virus contains a short, glycosylated amino-terminal domain, three membrane-spanning domains, and a long carboxy-terminal cytoplasmic domain. We show that E1 expressed from cDNA is targeted to the Golgi region, as it is in infected cells. E1 proteins with precise deletions of the first and second or the second and third membrane-spanning domains were glycosylated, thus suggesting that either the first or third transmembrane domain can function as an internal signal sequence. The mutant protein with only the first transmembrane domain accumulated intracellularly like the wild-type protein, but the mutant protein with only the third transmembrane domain was transported to the cell surface. This result suggests that information specifying accumulation in the Golgi region resides in the first transmembrane domain, and provides the first example of an intracellular membrane protein that is transported to the plasma membrane after deletion of a specific domain.
Gas-phase reactions for selective detection of the explosives TNT and RDX (2003)

Highly selective gas-phase reactions with ethyl vinyl ether (EVE) of major electron (EI) and chemical ionization (CI) fragment ions of the explosives TNT and RDX have been uncovered. The fragment ion of m/z 210 from TNT undergoes [4(+)+ 2] cycloaddition with EVE to form an oxo-iminium ion of m/z 282, which dissociates by acetaldehyde loss after a [1,5-H] shift to form a quinolynium ion of m/z 238. The fragment ion of m/z 149 from RDX reacts with EVE by a formal vinylation reaction, that is, the elusive cyclic adduct loses ethanol to yield a nitro-iminium ion of m/z 175, which reacts further with EVE to form a second cyclic product ion of m/z 247. Calculations and MS/MS experiments support the proposed structures. These highly characteristic reactions of diagnostic EI and CI fragment ions improve selectivity for TNT and RDX detection.
Adoptive cellular immunotherapy for EBV lymphoproliferative diseases (1997)

Reactivation of EBV (Epstein-Barr virus) after bone marrow transplantation can result in EBV-associated lymphoproliferative disease (EBV-LPD). We have administered donor-derived EBV-specific cytotoxic T lymphocytes (CTL) to patients who are at high risk of this complication after receiving a T-cell-depleted allograft from a matched unrelated or mismatched related donor. The cells were marked with the neo gene before infusion so that we could evaluate their persistence and efficacy. CTL infusion produced a virus-specific immune response to EBV that persisted for up to 2 years. None of the 36 patients who received prophylactic CTLs have developed EBV-LPD, compared with a cumulative risk of 14% in patients who did not receive this treatment. Strong evidence of clinically valuable immune activity comes from 6 of these 36 patients whose pre-CTL levels of EBV DNA were elevated to a degree strongly predictive of the onset of lymphoma. In each of these cases, the levels returned to baseline after CTL infusion. 2 patients who were treated for clinically evident EBV-LPD attained prolonged remission after CTL infusion and in situ hybridization and semiquantitative PCR showed that the gene-marked CTL had selectively accumulated at disease sites. The prophylactic CTL treatment lacked acute adverse effects, whereas 1 patient who received CTLs for bulky established disease developed initial tumor swelling and respiratory obstruction. We conclude that EBV-specific CTLs are a safe and effective prophylaxis for EBV lymphoma and can also eradicate established disease. This approach is now being extended to other viruses that produce post-transplant morbidity and to other EBV-associated malignancies.
Heat Transfer During Two-Phase Flow in Wellbores: Part I—Formation Temperature (1991)

ABSTRACT Heat loss from the wellbore fluid depends on the temperature distribution in the formation. Formation temperature distribution around a well was modeled by Ramey (1962) by assuming a vanishingly small wellbore radius. The assumption, while robust for some cases, could lead to unrealistic predictions of early-time behavior. This paper uses a rigorous model of heat transfer developed with consideration for the appropriate boundary conditions; that is, the heat transfer at the formation/wellbore interface is represented by the Fourier law of heat conduction. The superposition principle is used to account for the gradual change in heat transfer rate between the wellbore and the the formation. The results of the new analysis are in agreement with the classical work of Ramey for large times (dimensionless time, tD &amp;gt; 10). However, significant differences are noted between the proposed solution and that of Ramey’s log-linear approximation at small (tD &amp;lt; 1.0) times. These differences may have considerable effect on certain applications, such as static earth temperature estimation from temperature logs, and bottomhole temperature estimation for cyclic steam injection. We also present an approximate algebraic expression for the rigorous integral solution of dimensionless formation temperature, TD. This simplified expression is accurate for most engineering calculations. Use of this solution is shown in the second part of the paper where the wellbore fluid temperature distribution is computed during two-phase flow.
Activated Mutants of SHP-2 Preferentially Induce Elongation of Xenopus Animal Caps (2000)

In Xenopus ectodermal explants (animal caps), fibroblast growth factor (FGF) evokes two major events: induction of ventrolateral mesodermal tissues and elongation. The Xenopus FGF receptor (XFGFR) and certain downstream components of the XFGFR signal transduction pathway (e.g., members of the Ras/Raf/MEK/mitogen-activated protein kinase [MAPK] cascade) are required for both of these processes. Likewise, activated versions of these signaling components induce mesoderm and promote animal cap elongation. Previously, using a dominant negative mutant approach, we showed that the protein-tyrosine phosphatase SHP-2 is necessary for FGF-induced MAPK activation, mesoderm induction, and elongation of animal caps. Taking advantage of recent structural information, we now have generated novel, activated mutants of SHP-2. Here, we show that expression of these mutants induces animal cap elongation to an extent comparable to that evoked by FGF. Surprisingly, however, activated mutant-induced elongation can occur without mesodermal cytodifferentiation and is accompanied by minimal activation of the MAPK pathway and mesodermal marker expression. Our results implicate SHP-2 in a pathway(s) directing cell movements in vivo and identify potential downstream components of this pathway. Our activated mutants also may be useful for determining the specific functions of SHP-2 in other signaling systems.
Tutorial on Photoacoustic Microscopy and Computed Tomography (2008)

The field of photoacoustic tomography has experienced considerable growth in the past few years. Although several commercially available pure optical imaging modalities, including confocal microscopy, two-photon microscopy, and optical coherence tomography, have been highly successful, none of these technologies can provide penetration beyond ~1 mm into scattering biological tissues, because they are based on ballistic and quasi-ballistic photons. Heretofore, there has been a void in high-resolution optical imaging beyond this penetration limit. Photoacoustic tomography, which combines high ultrasonic resolution and strong optical contrast in a single modality, has broken through this limitation and filled this void. In this paper, the fundamentals of photoacoustics are first introduced. Then, scanning photoacoustic microscopy and reconstruction-based photoacoustic tomography (or photoacoustic computed tomography) are covered.
Magnetic Field-Controlled Microfluidic Transport (2001)

Several new forms of magnetohydrodynamic (MHD) flow occurring in the solution gap between two 250-microm-diameter Pt microdisk electrodes, oriented in a face-to-face geometry and immersed in a uniform magnetic field (1 T), are described. The MHD flow results from the Lorentz force generated by diffusion of electrochemically generated molecular ions through the magnetic field. Individual microscopic flow tubes ( approximately 50-microm radius) spanning the gap between the face-to-face electrodes are observed during the 1-e(-) reduction of nitrobenzene in acetonitrile solutions. The flow tubes extend up to approximately 2 cm in length and are stable for indefinite periods. Directional transport of the electrogenerated nitrobenzene radical anion over macroscopic distances within the flow tubes, with minimal diffusional broadening, is demonstrated using an ultramicroelectrode probe to map the convective flux of redox species. Pulsed MHD transport of small packets of molecules and the formation of large area (approximately 3 cm(2)), microscopically thin (25 microm) rotating sheets of solution are also demonstrated. The results suggest that electrochemical methods, in combination with magnetohydrodynamic principles, may be useful for external field-controlled microfluidic systems.
Telemedicine-Guided Carotid and Transcranial Ultrasound (2005)

Our pilot study showed the feasibility of TCD/CD by an inexperienced health professional guided by a sonographer via TM. Tests were completed within times comparable to outpatient setting in a vascular laboratory.
Antifibrinolytics for heavy menstrual bleeding (2000)

Antifibrinolytic therapy compared to placebo showed a significant reduction in mean blood loss (WMD -94.0 [-151.4, -36.5]) and significant change in mean reduction of blood loss (WMD -110.2 [-146. 5, -73.8]). This objective improvement was not mirrored by a patient perceived improvement in monthly menstrual blood loss (RR 2.5 [0.9, 7.3]) in the one study which recorded this outcome ( approximately approximately Edlund 1995 approximately approximately ). Antifibrinolytic agents were compared to only three other medical (non-surgical) therapies: mefenamic acid, norethisterone administered in the luteal phase and ethamsylate. In all instances, there was a significant reduction in mean blood loss (WMD -73.0 [-123.4, -22.6], WMD -111.0 [-178.5, -43.5] and (WMD -100 [-143.9, -56.1] respectively) and a strong, although non-significant trend in favour of tranexamic acid in the participants' perception of an improvement in menstrual blood loss. There were no significant differences in the frequency of reported gastrointestinal side effects with tranexamic acid when compared to either NSAIDs (RR 0.9 [0.4, 2.1], oral luteal phase progestagens (RR 0.4 [0.1, 1.2]) or ethamsylate (RR 0.88 [0.3, 2.9]) when these treatments were used for heavy menstrual bleeding. (ABSTRACT TRUNCATED)
Expansion and Activation of Natural Killer Cells for Cancer Immunotherapy (2009)

Natural killer (NK) cells can kill a wide range of cancer cells and are a promising tool for cell therapy of cancer. NK cells cytotoxicity is regulated by a balance between stimulatory and inhibitory signals. Interleukin-2 is known to increase NK cell cytotoxicity. Although many cytokines have been studied in efforts to induce durable NK cell expansions, most reports indicate a rather modest effect and the requirement for additional stimuli. We found that contact with the K562 myeloid leukemia cell line, genetically modified to express a membrane-bound form of interleukin-15 and the ligand for the costimulatory molecule 4-1BB, induced vigorous expansion of NK cells from peripheral blood. Based on these findings, we developed a method for large-scale clinical-grade expansion of NK cells. This method is currently used to expand allogeneic NK cells for infusion in patients with leukemia and solid tumors. We here summarize methods for expansion and activation of NK cells from human peripheral blood mononuclear cells as well as clinical-scale methods to produce NK cells for immunotherapy under Current Good Manufacturing Practices (cGMP) conditions.
Furanonaphthoquinones from Tabebuia ochracea ssp. neochrysanta (1996)

Activity-directed fractionation of the inner stem bark of Tabebuia ochracea ssp. neochrysanta led to the isolation of two new naphtho[2,3-b]furan-4,9-diones, the 5,8-dihydroxy-2-(1‘-hydroxyethyl) and 2-acetyl-7-methoxy-8-hydroxy derivatives, 1 and 2, together with four known naphthofurandiones.
Expression and Modulation of the Human Immunoglobulin A Fc Receptor (CD89) and the FcR γ Chain on Myeloid Cells in Blood and Tissue (2003)

CD89, the human immunoglobulin A (IgA) Fc receptor (FcR), is a potential target for antibody-based therapeutics, but little is known about its expression and modulation in vivo. In this study, we examined the expression pattern of CD89 and its signalling subunit, the FcR gamma chain, on circulating myeloid cells and in various tissues. Our results showed a wide tissue distribution of CD89+ cells. Thus, CD89+ cells were evident as clusters in tonsils and appendix and scattered in varying numbers in lymph nodes, kidney, liver, intestinal mucosa, bronchoalveolar lavage and peritoneal fluid. Most CD89+ cells were identified as neutrophils with high levels of CD89. A few recently emigrated macrophages (CD14low), weakly positive for CD89, were occasionally found in the tissues and more often in the peritoneal fluid. The level of CD89 on neutrophils in tissues and peripheral blood was similar, whereas on monocytes it was much lower in the tissues than in blood, and it was absent on CD14-/CD68+ intestinal lamina propria macrophages. Conversely, we detected much higher levels of the FcR gamma chain in monocytes than in neutrophils, but the FcR gamma chain was also downregulated in tissue macrophages as well as in in vitro-differentiated monocyte-derived macrophages and dendritic cells. The implications of our current findings on the biological functioning of CD89 are discussed.
Kinetic mechanism of isoprenylated protein methyltransferase. (1992)

The kinetic mechanism of the rod outer segment (ROS) isoprenylated protein methyltransferase was investigated. This S-adenosyl-L-methionine (AdoMet)-linked enzyme transfers methyl groups to carboxyl-terminal isoprenylated cysteine residues of proteins, generating methyl esters. The enzyme also processes simple substrates such as N-acetyl-S-farnesyl-L-cysteine (L-AFC). Initial studies showed that a ping-pong Bi Bi mechanism could be eliminated. In a ping-pong Bi Bi mechanism plots of 1/v versus 1/[substrate A] at different fixed substrate B concentrations are expected to yield a family of parallel lines whose slopes equal Km/Vmax. In fact, converging curves were found, which suggested a sequential mechanism. Dead-end inhibitors were used in order to further investigate the kinetic mechanism. S-Farnesylthioacetic acid is shown to be a dead-end competitive inhibitor with respect to the prenylated substrate L-AFC. On the other hand, S-farnesylthioacetic acid proved to be uncompetitive with respect to AdoMet, suggesting an ordered mechanism with AdoMet binding first. Further evidence for this mechanism came from product inhibition studies using the methyl ester of L-AFC (L-AFCMe) and S-adenosyl-L-homocysteine (AdoHcy). Since AdoMet binds first to the enzyme, one of the products (L-AFCMe or AdoHcy) should be a competitive inhibitor with respect to it. It could be shown that AdoHcy is a competitive inhibitor with respect to AdoMet, but L-AFCMe is a mixed-type inhibitor both with respect to AdoMet and to L-AFC. Therefore, AdoHcy combines with the same enzyme form as does AdoMet, and must be released from the enzyme last. Moreover, L-AFC and L-AFCMe must bind to different forms of the enzyme.
Induction of Intracellular Tau Aggregation Is Promoted by α-Synuclein Seeds and Provides Novel Insights into the Hyperphosphorylation of Tau (2011)

Intracytoplasmic proteinaceous inclusions, primarily composed of tau or α-synuclein (α-syn), are predominant pathological features of Alzheimer's disease (AD) and Parkinson's disease (PD), respectively. However, the coexistence of these pathological aggregates is identified in many neurodegenerative disorders, including spectrum disorders of AD and PD. Whereas α-syn can spontaneously polymerize into amyloidogenic fibrils, in vitro, tau polymerization requires an inducing agent. The current study presents a human-derived cellular model, in which recombinant, preformed α-syn fibrils cross-seed intracellular tau to promote the formation of neurofibrillary tangle-like aggregates. These aggregates were hyperphosphorylated, Triton insoluble, and thioflavin-S positive, either comingling with endogenously expressed α-syn aggregates or induced by only exogenously applied recombinant α-syn fibrils. Furthermore, filamentous, amyloidogenic tau took over the cellular soma, displacing the nucleus and isolating or displacing organelles, likely preventing cellular function. Although a significant proportion of wild-type tau formed these cellular inclusions, the P301L mutation in tau increased aggregation propensity resulting from α-syn seeds to over 50% of total tau protein. The role of phosphorylation on the development of these tau aggregates was investigated by coexpressing glycogen synthase kinase 3 β or microtubule-associated protein/microtubule affinity-regulating kinase 2. Expression of either kinase inhibited the formation of α-syn-induced tau aggregates. Analyses of phosphorylation sites suggest that multiple complex factors may be associated with this effect and that Triton-soluble versus Triton-insoluble tau may be independently targeted by kinases. The current work not only provides an exceptional cellular model of tau pathology, but also examines α-syn-induced tau inclusion formation and provides novel insights into hyperphosphorylation observed in disease.
Apoptosis by leukemia cell-targeted diphtheria toxin occurs via receptor-independent activation of Fas-associated death domain protein. (2003)

These data indicate that targeted toxins induce apoptosis by activating components of the death receptor pathway in a receptor-independent manner.
Purification and size‐selection of carbon nanotubes (1997)

A non‐destructive method for purifying carbon nanotubes produced by are discharge is described. The nanotubes, in the form of a kinetically stable colloidal dispersion in a water–surfactant solution, are separated from the nanoparticles by filtration. The Figure shows that purified nanotubes after two filtration steps. Through controlled flocculation, nanotube size election is also possible. magnified image
CHILLING SENSITIVITY IN PLANTS AND CYANOBACTERIA: The Crucial Contribution of Membrane Lipids (1996)

The contribution of membrane lipids, particularly the level of unsaturation of fatty acids, to chilling sensitivity of plants has been intensively discussed for many years. We have demonstrated that the chilling sensitivity can be manipulated by modulating levels of unsaturation of fatty acids of membrane lipids by the action of acyl-lipid desaturases and glycerol-3-phosphate acyltransferase. This review covers recent studies on genetic manipulation of these enzymes in transgenic tobacco and cyanobacteria with special emphasis on the crucial importance of the unsaturation of membrane lipids in protecting the photosynthetic machinery from photoinhibition under cold conditions. Furthermore, we review the molecular mechanism of temperature-induced desaturation of fatty acids and introduce our hypothesis that changes in the membrane fluidity is the initial event of the expression of desaturase genes.
Neural Network Approaches Versus Statistical Methods In Classification Of Multisource Remote Sensing Data (1990)

Neural network learning procedures and statistical classificaiton methods are applied and compared empirically in classification of multisource remote sensing and geographic data. Statistical multisource classification by means of a method based on Bayesian classification theory is also investigated and modified. The modifications permit control of the influence of the data sources involved in the classification process. Reliability measures are introduced to rank the quality of the data sources. The data sources are then weighted according to these rankings in the statistical multisource classification. Four data sources are used in experiments: Landsat MSS data and three forms of topographic data (elevation, slope, and aspect). Experimental results show that two different approaches have unique advantages and disadvantages in this classification application.
DECREASED EXPRESSION OF CELLULAR PROSTATIC ACID PHOSPHATASE INCREASES TUMORIGENICITY OF HUMAN PROSTATE CANCER CELLS (2001)

Cellular PAcP can down-regulate prostate cancer cell growth, at least partially by dephosphorylating c-ErbB-2/neu. Therefore, decreased cellular PAcP expression in cancer cells may be involved in prostate cancer progression.
Vaccination With Irradiated Autologous Tumor Cells Engineered to Secrete Granulocyte-Macrophage Colony-Stimulating Factor Augments Antitumor Immunity in Some Patients With Metastatic Non–Small-Cell Lung Carcinoma (2003)

Vaccination with irradiated autologous NSCLC cells engineered to secrete GM-CSF enhances antitumor immunity in some patients with metastatic NSCLC.
Preparation and characterization of the monoclonal antibodies against Japanese encephalitis virus. (1992)

Six mouse monoclonal antibodies (MoAbs) against Japanese encephalitis virus (JEV) were prepared and analyzed with indirect immunofluorescence assay (IFA), enzyme linked immunosorbent assay (ELISA), haemagglutination inhibition test (HI), neutralization test (NT), antibody dependent cell mediated cytotoxicity (ADCC) assay, antigenic site specific analysis and relative affinity measurement. These MoAbs could be divided into three classes by indirect immunofluorescence cross reactivity among four flaviviruses, 2H4, 2F2, and nG2 were type specific; 2D2 and mC3 were subgroup specific; and mG9 was family specific. 2H4 and 2F2 had higher neutralization activity, 2D2 and mC3 had the function of inducing ADCC effect, mG9 had higher titer in HI. The six MoAbs recognized five antigenic sites on JEV envelope glycoprotein, 2H4 and 2F2 recognized the same or very similar antigenic site and their relative affinity was ranked as: nG2 > 2H4 > 2D2 > mG9 > 2F2 > mC3.