gebhart/patrepeval huggingface dataset:
Isolation and characterization of propionyl-CoA carboxylase from normal human liver. Evidence for a protomeric tetramer of nonidentical subunits. (1980)

We have purified propionyl-CoA carboxylase from normal, postmortem human liver to homogeneity. The isolation procedure, which provided an approximately 3000-fold purification and an overall yield of 26%, employed initial centrifugation of a cetyltrimethylammonium bromide-treated homogenate, followed by sequential chromatographic separations using DEAE-cellulose, Blue Sepharose, and Bio-Gel A-1.5m. The native enzyme has a molecular weight of approximately 540,000 and is composed of nonidentical subunits (alpha and beta) of Mr = 72,000 and 56,000, respectively. When studied with analytical isoelectrofocusing techniques, it focuses as a single peak at pH 5.5. Each mole of native enzyme contains 4 mol of bound biotin, virtually all of which is found with the larger (alpha) subunit. The apparent Km values for ATP, propionyl-CoA, and bicarbonate are 0.08 mM, 0.29 mM, and 3.0 mM, respectively. The enzyme also catalyzes the carboxylation of acetyl-CoA and butyryl-CoA to a limited degree, but not that of crotonyl-CoA. Propionyl-CoA carboxylase is quite stable over a temperature range from -50--37 degrees C and over a pH range from 6.2 to 8.4. It has a broad pH optimum from pH 7.2 to 8.8. Limited proteolysis with trypsin results in slow, time-dependent deactivation of the enzyme with preferential cleavage of the smaller subunit. Antiserum prepared against the native enzyme is shown to be monospecific by immunodiffusion and immunoelectrophoresis.
ALK+ lymphoma: clinico-pathological findings and outcome. (1999)

A distinct pathologic entity (ALK+ lymphoma) that is characterized by expression of the anaplastic lymphoma kinase (ALK) protein has recently emerged within the heterogeneous group of CD30(+) anaplastic large-cell lymphomas. Information on clinical findings and treatment outcome of ALK+ lymphoma is still limited, and no data are available concerning the value of the International Prognostic Index when applied to this homogeneous disease entity. To clarify these issues, a recently developed monoclonal antibody ALKc (directed against the cytoplasmic portion of ALK) was used to detect expression of the ALK protein in paraffin-embedded biopsies from 96 primary, systemic T/null anaplastic large-cell lymphomas, and the ALK staining pattern was correlated with morphological features, clinical findings, risk factors (as defined by the International Prognostic Index), and outcome in 78 patients (53 ALK+ and 25 ALK-). Strong cytoplasmic and/or nuclear ALK positivity was detected in 58 of 96 ALCL cases (60.4%), and it was associated with a morphological spectrum (common type, 82.7%; giant cell, 3.5%; lymphohistiocytic, 8. 6%; and small cell, 5.2%) that reflected the ratio of large anaplastic elements (usually showing cytoplasmic and nuclear ALK positivity) to small neoplastic cells (usually characterized by nucleus-restricted ALK expression). Clinically, ALK+ lymphoma mostly occurred in children and young adults (mean age, 22.01 +/- 10.87 years) with a male predominance (male/female [M/F] ratio, 3.0) that was particularly striking in the second-third decades of life (M/F ratio, 6.5) and usually presented as an aggressive, stage III-IV disease, frequently associated with systemic symptoms (75%) and extranodal involvement (60%), especially skin (21%), bone (17%), and soft tissues (17%). As compared with ALK+ lymphoma, ALK- cases occurred in older individuals (mean age, 43.33 +/- 16.15 years) and showed a lower M/F ratio (0.9) as well as lower incidence of stage III-IV disease and extranodal involvement at presentation. Overall survival of ALK+ lymphoma was far better than that of ALK- anaplastic large-cell lymphoma (71% +/- 6% v 15% +/- 11%, respectively). However, within the good prognostic category of ALK+ lymphoma, survival was 94% +/- 5% for the low/low intermediate risk group (age-adjusted International Prognostic Index, 0 to 1) and 41% +/- 12% for the high/high intermediate risk group (age-adjusted International Prognostic Index, >/=2). Multivariate analysis identified ALK expression and the International Prognostic Index as independent variables that were able to predict survival among T/null primary, systemic anaplastic large-cell lymphoma. Thus, we suggest that such parameters should be taken into consideration for the design of future clinical trials.
Ion-irradiation-induced welding of carbon nanotubes (2002)

As recent transmission electron microscopy experiments demonstrate, electron irradiation can be used to create molecular junctions between carbon nanotubes. Employing empirical potential molecular dynamics, we study ion bombardment of crossed nanotubes as an alternative technique to join nanotubes. We demonstrate that ion irradiation should result in welding of crossed nanotubes, both suspended and deposited on substrates. We further discuss various experimental aspects of this method which may potentially be used for developing complicated networks of joined nanotubes.
Intracerebral grafting of neuronal cell suspensions. V. Behavioural recovery in rats with bilateral 6-OHDA lesions following implantation of nigral cell suspensions. (1983)

Bilateral 6-hydroxydopamine-induced lesions of the ascending forebrain dopamine neurones induce a behavioural syndrome in rats which includes profound aphagia, adipsia, akinesia and bilateral sensorimotor neglect. Such animals will die unless maintained by intragastric feeding. Three experiments are reported in which we have attempted to ameliorate this syndrome with single or multiple placements of nigral cell suspensions into the forebrains of rats with bilateral dopamine depletions. Although the grafts were efficient in reversing the sensorimotor and akinetic impairments, and produced a significant increase in eating, the grafted rats remained hypophagic and adipsic. The results indicate that although many components of the bilateral dopamine denervation syndrome can be reversed by intrastriatal nigral suspension grafts, the severe eating and drinking deficits remain unameliorated.
Ignition and maintenance of subsonic plasma waves in atmospheric pressure air by cw CO2 laser radiation and their effect on laser beam propagation (1975)

Laser supported combustion (LSC) waves, subsonically propagating plasma, are ignited from solid targets and maintained in atmospheric pressure air using focused high−power, as high as 15 kW, cw CO2 laser radiation. The intensity necessary to ignite LSC waves, Ii, is measured for steel and aluminum targets as a function of beam focal spot diameter and wind velocity transverse to the beam axis as is the intensity needed to maintain such waves in atmospheric pressure air, Im. In the absence of a transverse wind, the quantities Ii and Im are essentially identical for diameters smaller than 0.1 cm, but Ii is substantially larger at larger diameters. The reason for this is discussed in terms of the ignition mechanism itself. In the presence of a 20−m/sec transverse wind, Im and Ii are essentially identical at 0.2 cm, the largest diameter for which Ii was determined. The measurements of Im extend to 0.5 cm beam diameter and indicate, in the absence of the transverse wind, that while thermal conduction determines the value of Im at small (0.007 cm) beam diameters, radiative losses are important at the larger diameters considered. An interferometric technique is utilized to obtain spatially resolved LSC wave plasma properties, and the latter are used to calculate the decrease in focal spot laser intensity due to absorption and refraction by the plasma. The calculated results, as well as those obtained from independent experiments, indicate that while inverse bremsstrahlung absorption can account typically for a 50% loss in focal spot intensity, scattering or beam blooming by the plasma has a significantly greater effect as the LSC wave propagates away from the focal spot.
Sin recombinase fromStaphylococcus aureus: synaptic complex architecture and transposon targeting (2002)

The Sin recombinase from Staphylococcus aureus builds a distinctive DNA-protein synaptic complex to regulate strand exchange. Sin binds at two sites within an 86 basepair (bp) recombination site, resH. We propose that inverted motifs at the crossover site, and tandem motifs at the regulatory site, are recognized by structurally disparate Sin dimers. An essential architectural protein, Hbsu, binds at a discrete central site in resH. Positions of Hbsu-induced DNA deformation coincide with natural targets for Tn552 integration. Remarkably, Sin has the same topological selectivity as Tn3 and gammadelta resolvases. Our model for the recombination synapse has at its core an assembly of four Sin dimers; Hbsu plays an architectural role that is taken by two resolvase dimers in models of the Tn3/gammadelta synapse.
The CD3 zeta cytoplasmic domain mediates CD2-induced T cell activation. (1992)

CD2-mediated T lymphocyte activation requires surface expression of CD3-Ti, the T cell receptor (TCR) for antigen major histocompatibility complex protein. Given the importance of CD3 zeta in TCR signaling, we have directly examined the ability of the CD3 zeta cytoplasmic domain to couple CD2 to intracellular signal transduction pathways. A cDNA encoding a chimeric protein consisting of the human CD3 zeta cytoplasmic domain (amino acid residues 31-142) fused to the CD8 alpha extracellular and transmembrane domains (amino acid residues 1-187) was transfected into a CD2+CD3-CD8- variant of the human T cell line Jurkat. The resulting transfectants expressed the CD8 alpha/CD3 zeta chimeric receptor at the cell surface in the absence of other TCR subunits. Stimulation of these transfectants with anti-T11(2) + anti-T11(3) monoclonal antibodies (mAbs) initiated both a prompt cytosolic free calcium ([Ca2+]i) rise and protein tyrosine kinase activation. Stimulation with either intact anti-T11(2) + anti-T11(3) mAbs or purified F(ab')2 fragments resulted in interleukin 2 (IL-2) secretion. In contrast, control cell lines transfected with a cDNA encoding wild-type CD8 alpha, and thus lacking surface expression of the CD3 zeta cytoplasmic domain, failed to show any [Ca2+]i rise, protein tyrosine kinase activation, or IL-2 secretion after identical stimulation. These data directly establish the CD3 zeta cytoplasmic domain as a necessary and sufficient component of the CD3-Ti complex involved in T lymphocyte activation through CD2. Moreover, they show that CD2 signaling can function in the absence of Fc receptors.
Amyloid-β binds catalase with high affinity and inhibits hydrogen peroxide breakdown (1999)

Amyloid-β (Aβ) specifically bound purified catalase with high affinity and inhibited catalase breakdown of H2O2. The Aβ-induced catalase inhibition involved formation of the inactive catalase Compound II and was reversible. Catalase ↔ Aβ interactions provide rapid functional assays for the cytotoxic domain of Aβ and suggest a mechanism for some of the observed actions of Aβ plus catalase in vitro.
TheALD6 gene ofSaccharomyces cerevisiae encodes a cytosolic, Mg2+-activated acetaldehyde dehydrogenase (1997)

The deduced translation product of an open reading frame on the left arm of chromosome XVI of Saccharomyces cerevisiae, with the systematic name of YPL061w, is 500 amino acids in length and shares significant homology with aldehyde dehydrogenases. Amino acids 2 to 16 of the protein encoded by YPL061w were found to be identical to the N-terminal 15 amino acids of the purified cytosolic, Mg(2+)-activated acetaldehyde dehydrogenase (ACDH) of S. cerevisiae. This enzyme is thought to be involved in the production of acetate from which cytosolic acetyl-CoA is then synthesized. Deletion of YPL061w was detrimental to the growth of haploid strains of yeast; an analysis of one deletion mutant revealed a maximum specific growth rate (in complex medium containing glucose) of one-third of that displayed by the wild-type strain. Mutants deleted in YPL061w were also unable to use ethanol as a carbon source. As expected, the cytosolic, Mg(2+)-activated ACDH activity had been lost from the mutants, although the mitochondrial, K(+)-activated ACDH was readily detected.
Transformation of Acidiphilium by electroporation and conjugation (1992)

Two techniques, electroporation and conjugation, have been used to introduce the RK2-based broad-host-range plasmids pRK415 and pLAFR3 into strains of the bacterial genus Acidiphilium. Using electroporation, cells were also transformed with a series of chimeric plasmids constructed by cloning cryptic Acidiphilium plasmids into the Escherichia coli vector pBR328. Various parameters affecting electroporation were investigaed. Transformation efficiency varied widely with different recipient strains. Growth at an elevated temperature (37 °C) prior to electroporation increased transformation efficiency 10-fold compared with growth at 32 °C. For three strains tested, optimum transformation efficiency was obtained with field strengths of 10–15 kV/cm. Transformation efficiency increased linearly with increasing DNA concentration up to 10 μg/mL. Transformation efficiencies in these experiments ranged up to 10 4 transformants/μg DNA. Mobilization of pRK415 and pLAFR3 from E. coli strain S17.1 into several Acidiphilium strains was achieved following incubation for 3 h on nutrient agar medium (pH 7.0). Conjugation frequencies in the range of 10 −5 –10 −9 per recipient cell were obtained. Conjugation frequency was also dependent on recipient strain. Key words: acidophilic bacteria, endogenous plasmids, broad-host-range plasmids.
Thrombosis and platelets: an update (2016)

Haemostasis and thrombosis are complex, multifactorial processes. There is an evolving understanding of the mechanisms influencing vascular occlusion and the role of inflammation and immunity. Despite major advances in elucidating the mechanistic pathways mediating platelet function and thrombosis, challenges in the treatment of vascular occlusive diseases persist. Pharmacological advances have greatly affected thrombotic outcomes, but this has led to the unwanted side effect of bleeding. Detailed assessment of the impact of non-thrombotic diseases on haemostasis and thrombosis is necessary to better evaluate thrombotic risk and establish optimal treatment. This review will focus on recent advances in understanding the contribution of evolving risk factors to thrombosis.
Regional activation of chromosomal arm 7q with and without gene amplification in taxane‐selected human ovarian cancer cell lines (2005)

Taxanes are important drugs in the treatment of ovarian and other cancers, but their efficacy is limited by intrinsic and acquired drug resistance. Expression of the multidrug transporter P-glycoprotein, encoded by the MDR1 (ABCB1) gene, is one of the causes of clinical drug resistance to taxanes. To study the mechanisms of MDR1 activation related to taxanes, we established 11 multidrug-resistant variants from six ovarian cancer cell lines by continuous exposure to either paclitaxel or docetaxel. We profiled gene expression and gene copy number alterations in these cell lines using cDNA microarrays and identified a cluster of genes coactivated with MDR1 in 7q21.11-13. Regional activation was evident in nine resistant variants displaying a coexpression pattern of up to 22 genes over an 8-Mb area, including SRI, MGC4175, CLDN12, CROT, and CDK6. In six of these variants, regional activation was driven by gene copy number alterations, with low-level gains or high-level amplifications spanning the involved region. However, three variants displayed regional increases in gene expression even without concomitant gene copy number changes. These results suggest that regional gene activation may be a fundamental mechanism for acquired drug resistance, with or without changes in gene dosage. In addition to numerical and structural chromosomal changes driven by genome instability in cancer cells, other mechanisms might be involved in MDR1 regional activation, such as chromatin remodeling and DNA or histone modifications of the 7q21 region.
Unusually large von Willebrand factor multimers increase adhesion of sickle erythrocytes to human endothelial cells under controlled flow. (1987)

The interactions of normal erythrocytes and erythrocytes from patients having hemoglobin S hemoglobinopathies with normal human endothelial cells (EC) were investigated under flow conditions. When EC supernatant, containing 2.8-11.0 U/dl of von Willebrand factor (vWF) antigen and vWF multimeric forms larger than those present in normal plasma, was the red blood cell (RBC)-suspending medium instead of serum-free medium (SFM), the adhesion of sickle RBC, but not normal RBC, to endothelial cells was greatly increased (range of enhancement of sickle RBC adhesion, 2- to 27-fold). Adhesion of sickle RBC to endothelial cells was reduced to near serum-free levels when EC supernatant was immunologically depleted of vWF forms. Sickle RBC suspended in SFM containing 200 U/dl of purified vWF multimers of the type found in normal human plasma or 300 micrograms/ml human fibronectin were only slightly more adhesive to endothelial cells than sickle RBC suspended in SFM alone. These data indicate that unusually large vWF multimers produced by endothelial cells are potent mediators of the adhesion of sickle erythrocytes to endothelial cells. Vaso-occlusive crises in sickle cell anemia may be caused, at least in part, by adhesive interactions between the abnormal surfaces of sickle RBC and the endothelium after the release of unusually large vWF multimeric forms from stimulated or damaged endothelial cells.
Irreversible Electroporation: Implications for Prostate Ablation (2007)

Percutaneous prostate cryo-ablation has become an accepted treatment for primary prostate cancer. Thermal tissue ablation based on cold, however, does have some distinct limitations. These include, variable damage at the cryo lesions margin, injury to adjacent structures such as rectum, urethra and NVB (neurovascular bundle), and long procedure time due to the need for multiple freeze thaw cycles, that have limited the acceptance of this modality. Irreversible electroporation IRE, is a new non-thermal ablation modality that uses short pulses of DC electric current to create irreversible pore in the cell membrane, thus, causing cell death. This method theoretically should have significant advantages in ablating prostate tissue. Six males dogs had their prostates treated using IRE. Pulses were applied using a DC generator that delivered pulses in the microsecond range of duration, with a variable pulse interval and voltage range. IRE probes were placed percutaneously or trans-rectally using trans-rectal ultrasound guidance. In one of the dogs, the lesions were made purposely to include the rectum, urethra, and neurovascular bundle (NVB). Subjects were followed for 1 to 14 days before sacrifice. IRE lesions in the prostate had unique characteristics compared to thermal lesions. The margins of the IRE lesions was very distinct with a narrow zone of transition from normal to complete necrosis, there was complete destruction within the IRE lesion, and rapid resolution of the lesions with marked shrinkage within two weeks. Structures such as urethra, vessels, nerves, and rectum were unaffected by the IRE application. IRE lesions have characteristics that are distinctly different than thermal lesions. The differences could be very advantageous in a clinical setting, improving the results and acceptance of prostate ablation.
Preproglucagon gene expression in pancreas and intestine diversifies at the level of post-translational processing. (1986)

Glucagon is a pancreatic hormone of 29 amino acids that regulates carbohydrate metabolism and glicentin is an intestinal peptide of 69 amino acids that contains the sequence of glucagon flanked by peptide extensions at the amino and carboxy termini. The glucagon gene encodes a precursor containing glucagon and two additional, structurally related, glucagon-like peptides separated by an intervening peptide. These peptides are encoded in separate exons. To determine whether the pancreatic and intestinal forms of glucagon arise by alternative RNA and/or protein processing, we used antisera to synthetic glucagon-like peptides and exon-specific, complementary oligonucleotides for analyses of proteins and mRNAs in pancreatic and intestinal extracts. Preproglucagon mRNAs are identical, but different and highly specific peptides are liberated in the two tissues. Immunocytochemistry shows colocalization of glucagon and the two glucagon-like peptides in identical cells. We conclude that diversification of preproglucagon gene expression occurs at the level of cell-specific post-translational processing.
Transmitter redundancy for blind estimation and equalization of time- and frequency-selective channels (2000)

Joint mitigation of time- and frequency-selective fading is an important and challenging problem in mobile communications. Relying on transmitter-induced redundancy, we propose novel channel estimation and symbol recovery approaches for blind identification and equalization of time- and frequency-selective channels, where the time variation is modeled deterministically by a basis expansion. The resulting statistical algorithm enables the usage of a single antenna, dispenses with channel disparity conditions of existing approaches, and allows channel order overestimation. In addition, new deterministic algorithms for generalized OFDM systems are introduced that produce reliable estimates with few data points at high SNR's. Simulations illustrate the approaches developed.
Review on solving the inverse problem in EEG source analysis (2008)

In this primer, we give a review of the inverse problem for EEG source localization. This is intended for the researchers new in the field to get insight in the state-of-the-art techniques used to find approximate solutions of the brain sources giving rise to a scalp potential recording. Furthermore, a review of the performance results of the different techniques is provided to compare these different inverse solutions. The authors also include the results of a Monte-Carlo analysis which they performed to compare four non parametric algorithms and hence contribute to what is presently recorded in the literature. An extensive list of references to the work of other researchers is also provided. This paper starts off with a mathematical description of the inverse problem and proceeds to discuss the two main categories of methods which were developed to solve the EEG inverse problem, mainly the non parametric and parametric methods. The main difference between the two is to whether a fixed number of dipoles is assumed a priori or not. Various techniques falling within these categories are described including minimum norm estimates and their generalizations, LORETA, sLORETA, VARETA, S-MAP, ST-MAP, Backus-Gilbert, LAURA, Shrinking LORETA FOCUSS (SLF), SSLOFO and ALF for non parametric methods and beamforming techniques, BESA, subspace techniques such as MUSIC and methods derived from it, FINES, simulated annealing and computational intelligence algorithms for parametric methods. From a review of the performance of these techniques as documented in the literature, one could conclude that in most cases the LORETA solution gives satisfactory results. In situations involving clusters of dipoles, higher resolution algorithms such as MUSIC or FINES are however preferred. Imposing reliable biophysical and psychological constraints, as done by LAURA has given superior results. The Monte-Carlo analysis performed, comparing WMN, LORETA, sLORETA and SLF, for different noise levels and different simulated source depths has shown that for single source localization, regularized sLORETA gives the best solution in terms of both localization error and ghost sources. Furthermore the computationally intensive solution given by SLF was not found to give any additional benefits under such simulated conditions.