gebhart/patrepeval huggingface dataset:
Characterisation of the diol dehydratasepduoperon ofLactobacillus collinoides (2002)

The three genes (pduCDE) encoding the diol dehydratase of Lactobacillus collinoides were sequenced. They exhibited strong identities with the ddrABC and pduCDE genes of Klebsiella oxytoca and Salmonella enterica, respectively. These genes are part of a putative operon with at least four other genes. An eighth open reading frame was identified as homologous to the pocR gene (encoding the operon regulatory protein). Although the enzyme was detected in exponential growth phase, PduCDE activity was increased at the end of exponential phase in presence of 1,2-propanediol.
Hematopoietic Reconstitution of Syngeneic Mice with a Peripheral Blood-Derived, Monoclonal CD34-, Sca-1+, Thy-1low, c-kit+ Stem Cell Line (1999)

Previous work had revealed that a CD34- fibroblast-like cell is the earliest hematopoietic progenitor population. This cell type is able to differentiate into hematopoietic progeny of all lineages and circulates in the peripheral blood, from where it can be isolated by IL-6-mediated plastic adherence. We isolated peripheral blood-derived mononuclear cells (MNC) from male CBA mice and established in vitro a fibroblast-like, adherent growing cell layer. Cells were immortalized by SV-40 transfection for cellular cloning. Monoclonal fibroblast-like cell clones were established, and the surface expression of early stem cell markers was determined by flow cytometry. Clones were CD34-, Sca-1+, Thy-1(low), and c-kit+. Lethally irradiated female CBA mice were successfully transplanted with a fibroblast-like cell clone, R-M26/2-1. After syngeneic transplantation, peripheral blood counts were back to normal in transplanted mice on days 15-20, and fluorescence in situ hybridization (FISH) revealed the sole presence of male hematopoietic cells in the BM of female recipients at weeks 7, 9, 11, and 16 after transplantation. Immunohistochemistry for the expression of CD34, Sca-1, Thy-1, and c-kit showed the presence of the phenotype of the transplanted stem cell clone along the bone spicules in the marrow cavity, giving rise to HPC of all lineages. In summary, we have shown that a CD34-, Sca-1+, Thy-1(low), and c-kit+ fibroblast-like cell is consistent with the phenotype of the earliest hematopoietic and repopulating stem cell and can be isolated from peripheral blood cells.
Parallelization of Bresenham's line and circle algorithms (1990)

Parallel algorithm for line and circle drawing that are based on J.E. Bresenham's line and circle algorithms (see Commun. ACM, vol.20, no.2, p.100-6 (1977)) are presented. The new algorithms are applicable on raster scan CRTs, incremental pen plotters, and certain types of printers. The line algorithm approaches a perfect speedup of P as the line length approaches infinity, and the circle algorithm approaches a speedup greater than 0.9P as the circle radius approaches infinity. It is assumed that the algorithm are run in a multiple-instruction-multiple-data (MIMD) environment, that the raster memory is shared, and that the processors are dedicated and assigned to the task (of line or circle drawing).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Mechanism by Which Orally Administered β-1,3-Glucans Enhance the Tumoricidal Activity of Antitumor Monoclonal Antibodies in Murine Tumor Models (2004)

Antitumor mAb bind to tumors and activate complement, coating tumors with iC3b. Intravenously administered yeast beta-1,3;1,6-glucan functions as an adjuvant for antitumor mAb by priming the inactivated C3b (iC3b) receptors (CR3; CD11b/CD18) of circulating granulocytes, enabling CR3 to trigger cytotoxicity of iC3b-coated tumors. Recent data indicated that barley beta-1,3;1,4-glucan given orally similarly potentiated the activity of antitumor mAb, leading to enhanced tumor regression and survival. This investigation showed that orally administered yeast beta-1,3;1,6-glucan functioned similarly to barley beta-1,3;1,4-glucan with antitumor mAb. With both oral beta-1,3-glucans, a requirement for iC3b on tumors and CR3 on granulocytes was confirmed by demonstrating therapeutic failures in mice deficient in C3 or CR3. Barley and yeast beta-1,3-glucan were labeled with fluorescein to track their oral uptake and processing in vivo. Orally administered beta-1,3-glucans were taken up by macrophages that transported them to spleen, lymph nodes, and bone marrow. Within the bone marrow, the macrophages degraded the large beta-1,3-glucans into smaller soluble beta-1,3-glucan fragments that were taken up by the CR3 of marginated granulocytes. These granulocytes with CR3-bound beta-1,3-glucan-fluorescein were shown to kill iC3b-opsonized tumor cells following their recruitment to a site of complement activation resembling a tumor coated with mAb.
The Affinity of EBNA1 for Its Origin of DNA Synthesis Is a Determinant of the Origin's Replicative Efficiency (2008)

Epstein-Barr virus (EBV) replicates its genome as a licensed plasmid in latently infected cells. Although replication of this plasmid is essential for EBV latent infection, its synthesis still fails for 16% of the templates in S phase. In order to understand these failures, we sought to determine whether the affinity of the initiator protein (EBNA1) for its binding sites in the origin affects the efficiency of plasmid replication. We have answered this question by using several engineered origins modeled upon the arrangement of EBNA1-binding sites found in DS, the major plasmid origin of EBV. The human TRF2 protein also binds to half-sites in DS and increases EBNA1's affinity for its own sites; we therefore also tested origin efficiency in the presence or absence of these sites. We have found that if TRF2-half-binding sites are present, the efficiency of supporting the initiation of DNA synthesis and of establishing a plasmid bearing that origin directly correlates with the affinity of EBNA1 for that origin. Moreover, the presence of TRF2-half-binding sites also increases the average level of EBNA1 and ORC2 bound to those origins in vivo, as measured by chromatin immunoprecipitation. Lastly, we have created an origin of DNA synthesis from high-affinity EBNA1-binding sites and TRF2-half-binding sites that functions severalfold more efficiently than does DS. This finding indicates that EBV has selected a submaximally efficient origin of DNA synthesis for the latent phase of its life cycle. This enhanced origin could be used practically in human gene vectors to improve their efficiency in therapy and basic research.
BRI3 associates with SCG10 and attenuates NGF-induced neurite outgrowth in PC12 cells (2008)

In a yeast two-hybrid screen, we identified the microtubule-destabilizing protein SCG10 as a potential effector protein of BRI3. The association was verified using GST pull-down, Co-IP, and their perinuclear co-localization. The analysis of in vitro microtubule polymerization/depolymerization showed that the binding of BRI3 to SCG10 effectively blocked the ability of SCG10 to induce microtubule disassembly, as determined by turbidimetric assays. In intact PC12 cells, BRI3 exhibited the ability to stabilize the microtubule network and attenuate the microtubuledestabilizing activity of SCG10. Furthermore, co-expression of BRI3 with SCG10 attenuated SCG10-mediated PC12 cell neurite outgrowth induced by NGF. These results identify a novel connection between a neuron-specific BRI protein and the cytoskeletal network, suggesting possible roles of BRI3 in the process of neuronal differentiation.
Flow‐dependent concentration polarization of plasma proteins at the luminal surface of a semipermeable membrane (1999)

The effect of steady shear flow on concentration polarization of plasma proteins and lipoproteins at the luminal surface of a semipermeable vessel wall was studied experimentally using suspensions of these molecules in a cell culture medium and a semipermeable membrane dialysis tube which served as a model of an implanted vascular graft or an artery. The study was carried out by flowing a cell culture medium containing fetal calf serum or bovine plasma lipoproteins or bovine albumin through a 7.5 mm diameter, 60 mm-long dialysis tube in steady flow under a physiologic mean arterial perfusion pressure of 100 mmHg, and measuring the filtration velocity of water (cell culture medium) at the vessel wall which varied as a consequence of the change in concentration of plasma protein particles at the luminal surface of the semipermeable membrane dialysis tube. It was found that for perfusates containing plasma proteins and/or lipoproteins, filtration velocity of water was the lowest in the absence of flow, and it increased or decreased as the flow rate (hence wall shear rate) increased or decreased from a certain non-zero value, indicating that surface concentration of protein particles varied reversibly as a direct function of flow rate. It was also found that at particle concentrations equivalent to those found in a culture medium containing serum at 5% by volume, plasma lipoproteins which were much smaller in number and lower in concentration but larger in size than albumin, had a much larger effect on the filtration velocity of water than albumin. These findings were very much the same as those previously obtained with a cultured endothelial cell monolayer, strongly suggesting that the flow-dependent variation in filtration velocity of water at a vessel wall results from a physical phenomenon, that is, flow-dependent concentration polarization of low density lipoproteins at the luminal surface of the endothelial cell monolayer.
KINETIC MEASUREMENTS OF CELLULASE ACTIVITY ON INSOLUBLE SUBSTRATES USING DISODIUM 2,2' BICINCHONINATE (1998)

Determinations of cellulase activity using insoluble substrates have typically required long incubation times and significant amounts of enzyme. Utilizing disodium 2,2′-bicinchoninate, an assay has been developed to measure the initial production of reducing groups released during cellulase hydrolysis of insoluble, regenerated cellulose. The procedure permits the determination of total, soluble and insoluble reducing groups from a single reaction mixture under initial velocity conditions (< 3% hydrolysis). We report the applicability of this method to determinations of enzyme activity and for average molecular weight calculations of substrates. The K m values for Trichoderma reesei EG I, EG II, CBH I and CBH II are reported using phosphoric acid swollen cellulose (average DP 166) as a substrate. Procedures for preparation of uniform cellulose suspensions are described.
Light Scattering and Trapping in Different Thin Film Photovoltaic Devices (2009)

Light trapping in different thin film technologies is investigated in the context of the European integrated project ATHLET since it allows for thinner devices and thus for reduction of costs for absorber material preparation as well as for advanced multi-junction solar cells. In silicon technology, rough interfaces are typically introduced by roughening of substrates, transparent conducting oxides (TCOs) and/or reflectors at the back side to scatter the light into the absorber material. Well known rough TCOs, plasma-textured poly-Si as well as rough Cu(In,Ga)Se2 (CIGS) absorbers are used as source for light scattering in microcrystalline silicon solar cells and compared regarding their surface roughness. The results prove that CIGS and poly silicon solar cells provide efficient light scattering by the surface features of the rough absorber.
Detection of Previous Proximal Venous Thrombosis With Doppler Ultrasonography and Photoplethysmography (1989)

To evaluate the reliability of two noninvasive tests, the photoplethysmograph (PPG) and venous Doppler ultrasound, in determining the presence or absence of previous proximal deep vein thrombosis (DVT), we performed a blinded retrospective cohort study of patients with objectively confirmed (DVT+) or refuted (DVT-) previous episodes of suspected DVT. Twenty-nine of 33 DVT+ patients had abnormal PPG and/or reflux by venous Doppler ultrasound, whereas 39 of 49 DVT- patients had normal PPG and no Doppler reflux (sensitivity, 88%; specificity, 80%). Of 33 DVT+ patients, 20 had abnormal Doppler results (sensitivity, 61%), in contrast to 46 of 49 DVT- patients with normal results (specificity, 94%). Moreover, 23 of 33 DVT+ patients showed abnormal PPG results (sensitivity, 70%), whereas 40 of 49 DVT- patients had normal PPG (specificity, 82%). Based on our findings, the presence of Doppler reflux is specific for previous proximal DVT, whereas a combination of normal PPG and Doppler ultrasound is reliable for excluding previous proximal DVT. Abnormal PPG with normal Doppler ultrasound does not reliably predict the presence or absence of previous DVT. However, this occurred in only 16 of 82 patients. Therefore, the combination of PPG and venous Doppler ultrasound can reliably predict the presence or absence of previous proximal DVT in most patients.
Chemomechanical Polishing of Silicon Carbide (1997)

In an effort to improve silicon carbide (SiC) substrates surfaces prior to epitaxial growth, two chemomechanical polishing (CMP) techniques were investigated and the results were compared with a mechanical polishing procedure involving various grades of diamond paste. This work focused on silicon‐terminated (0001) SiC surfaces.The two CMP techniques utilized (i) chromium oxide(III) abrasives and (ii) colloidal silica polishing slurry. The best surfaces were obtained after colloidal silica polishing under conditions that combined elevated temperatures (∼55°C) with a high slurry alkalinity (pH > 10) and a high solute content. Cross‐sectional transmission electron microscopy showed no observable subsurface damage, and atomic force microscopy showed a significant reduction in roughness compared to commercial diamond‐polished wafers. Growth experiments following colloidal silica polishing yielded a much improved film surface morphology.
Cryopreservation of Human Hematopoietic Cells with Membrane Stabilizers and Bioantioxidants as Additives in the Conventional Freezing Medium (2001)

Cord blood (CB) and fetal liver (FL) cells are two alternative sources of human hematopoietic stem cells. Optimization of cryopreservation protocols is an important aspect in the banking of these tissues. Out of the multiple factors responsible for cryodamage of cells, membrane leakage and oxygen free-radical generation have been shown to contribute substantially toward the process. We have studied the effect of certain additives, like membrane stabilizers and bioantioxidants, to the conventional freezing medium on viability, nucleated cell recovery, and clonogenic potential of frozen cells. Our results show that trehalose, a membrane stabilizer, when used in combination with 10% dimethyl sulfoxide (DMSO) affords better cryoprotection as evidenced by significantly increased colony formation as compared to 10% DMSO alone. The cryoprotection afforded by trehalose persists at least for 1.5 years and there is no bias toward protection of a particular lineage. We also found that this increased cryoprotective effect of trehalose is seen both at -196 degrees C and -80 degrees C storage temperatures. Addition of taurine, an amino acid, another membrane stabilizer, and a natural cryoprotectant to the traditional freezing medium also results in beneficial effect. Of the three bioantioxidants tested, i.e., ascorbic acid, alpha-tocopherol acetate, and catalase, catalase shows maximum cryoprotective effect both at -196 degrees C and at -80 degrees C. Because the mode of cryoprotective action of catalase and trehalose are totally different, we tried a combination of these two compounds along with 10% DMSO. At -196 degrees C the protection afforded by the combination was significantly better than that afforded by individual components. At -80 degrees C, however, the combination did not give any added protection as compared to the individual single additives, although it was significantly better than 10% DMSO alone. These results indicate that the addition of membrane stabilizers and antioxidants to the conventional freezing medium may help to improve post thaw recovery of hematopoietic cells.
Adjuvant immunotherapy for melanoma (1984)

Adjuvant immunotherapy was administered to 84 lymph-node-negative and 25 lymph-node-positive melanoma patients. This active specific homologous cell protein preparation was given after aggressive surgery and given over 2 years. Projected and observed survival rates are presented as well as other clinical and pathologic characteristics such as female-to-male ratio, site of primary, level and depth of invasion. The projected 5-year survival rates are 90% for all stage I with 89% for females and 94% for males. Lower extremity stage I projected 5-year survival rate was 88% for all, 87% for females, and 100% for males. The projected 5-year survival rate for stage II was 68% overall and 100% for lower extremity. Only two of five patients with an unknown primary have expired. All of these results are improved over expected survival. Hopefully a randomized prospective study will be stimulated to ascertain the basis for this improvement.
Cloning and sequencing of phospholipase B gene from the yeastTorulaspora delbrueckii (1994)

The extracellular phospholipase B gene from baker's yeast Torulaspora delbrueckii was cloned and sequenced. Analysis of DNA sequence data revealed an open reading frame (ORF) encoding a 649-amino acid protein, that included amino acid sequences obtained from the purified enzyme. Comparison of these sequence data with the N-terminal amino acid sequence of the enzyme indicated that this secreted protein is synthesized as a large precursor with a 21-amino acid N-terminal extension to the mature enzyme of 628 amino acids. A homology search was carried out between phospholipase B from T. delbrueckii and Penicillium notatum. The deduced amino acid sequence of the cloned phospholipase B was homologous (about 50% identity) to phospholipase B from P. notatum, and contained six conserved regions. The transcriptional level of mRNA of the phospholipase B gene was higher in the cells from early exponential and stationary phases.
TGF-beta receptors: structure and function. (1994)

The transforming growth factor beta (TGF-beta) superfamily of dimeric polypeptide growth factors regulate cell growth and differentiation and play important roles in embryonic development and the immune response. The molecular cloning of three types of high affinity cell-surface receptors (type I, type II and type III) for these growth factors provide insights into their poorly understood mechanisms of action. Here we focus on the structure of these receptors and on the complex interactions which occur between different receptors that are necessary for ligand-induced signal transduction. The type I and type II receptors are both related transmembrane serine/threonine kinase receptors which may hetero-oligomerize to transduce proper signals. The type III receptor modulates the binding of ligands to the signaling complex of type I and type II receptors. These findings suggest that serine/threonine phosphorylation and heteromeric receptor interactions are important elements of TGF-beta induced signaling.
Benefits and Risks in Malaria Control (2005)

The Reports by S. Blanford et al. (“Fungal pathogen reduces potential for malaria transmission,” 10 June, p. [1638][1]) and E.-J. Scholte et al. (“An entomopathogenic fungus for control of adult African malaria mosquitoes,” 10 June, p. [1641][2]) identify the fungus Metarhizium anisopliae as
Photoinduced electron-transfer kinetics of singly labeled ruthenium bis(bipyridine) dicarboxybipyridine cytochrome c derivatives (1989)

Cytochrome c derivatives labeled at specific lysine amino groups with ruthenium bis(bipyridine) dicarboxybipyridine [RuII(bpy)2(dcbpy)] were prepared by using the procedure described previously [Pan, L. P., Durham, B., Wolinska, J., & Millett, F. (1988) Biochemistry 27, 7180-7184]. Four additional singly labeled derivatives were purified, bringing the total number to 10. These derivatives have a strong luminescence emission centered at 662 nm arising from the excited state, RuII*. Transient absorption spectroscopy was used to directly measure the rate constants for the photoinduced electron-transfer reaction from RuII* to the ferric heme group (k1) and for the thermal back-reaction from the ferrous heme group to RuIII (k2). The rate constants were found to be k1 = 14 X 10(6) s-1 and k2 = 24 X 10(6) s-1 for the derivative modified at lysine 72, which has a distance of 8-16 A between the ruthenium and heme groups. Similar rate constants were found for the derivatives modified at lysines 13 and 27, which have distances of 6-12 A separating the ruthenium and heme groups. The rate constants were significantly slower for the derivatives modified at lysine 25 (k1 = 1 X 10(6) s-1, k2 = 1.5 X 10(6) s-1) and lysine 7 (k1 = 0.3 X 10(6) s-1, k2 = 0.5 X 10(6) s-1), which have distances of 9-16 A. Transients due to photoinduced electron transfer could not be detected for the remaining derivatives, which have larger distances between the ruthenium and heme groups.(ABSTRACT TRUNCATED AT 250 WORDS)
Role of interleukin 6 for differential responsiveness of naive and memory CD4+ T cells in CD2-mediated activation. (1990)

The present study was undertaken to elucidate different requirements for CD2-mediated activation of naive (CD45RO-) and memory (CD45RO+) CD4+ T cells. A mitogenic combination of anti-CD2 (anti-T11(2) and anti-T11(3] mAbs could effectively induce the proliferation of memory CD4+ T cells even in the absence of monocytes. In marked contrast, naive CD4+ T cells did not disclose any proliferative responses to anti-CD2 mAbs, when monocytes were absent in culture. This differential responsiveness of naive and memory CD4+ T cells appeared to be related largely to a difference in IL-6-producing ability between both populations. IL-6 among monocyte-derived cytokines could correct unresponsiveness of naive CD4+ T cells to anti-CD2 stimulation. Unlike naive CD4+ T cells, memory CD4+ T cells produced IL-6 by themselves, with its mRNA being expressed on anti-CD2 stimulation. Anti-IL-6R mAb significantly inhibited proliferation of memory CD4+ T cells seen in the anti-CD2-stimulated cultures without monocytes, indicating the involvement of their own production of IL-6 in CD2-mediated activation. The results suggest an essential role of IL-6 for triggering of CD4+ T cells via the CD2 molecule.