gebhart/patrepeval huggingface dataset:
Engineering the acetyl‐CoA transportation system of candida tropicalis enhances the production of dicarboxylic acid (2005)

Dicarboxylic acids (DCAs) can be obtained by oxidizing alkanes by Candida tropicalis. Through alpha-monocarboxylic acids (MCAs), alpha- and omega-oxidation yield alpha- or omega-DCAs, respectively. However, both MCAs and DCAs may be degraded to acetyl-CoA by beta-oxidation, resulting in a limited DCA yield. Acetyl-CoA can be transported into the mitochondrion for the TCA cycle by carnitine acetyltransferase (CAT), by which the energy generation and beta-oxidation are connected. In this paper, we present a method to reconstruct the metabolic pathway by inhibiting the acetyl-CoA transportation system. Metabolic engineering is applied on the acetyl-CoA transportation system, but not the key enzymes in beta-oxidation. Starting with the original strain W10-1, cat heterozygote CZ-15 and cat homozygote CKC-11 were obtained by gene knockout. The CAT specific activity in CZ-15 was about 50% lower than that in W10-1, resulting in a 21.0% increase of the DCA concentration, and a 12% increase of the molar conversion of alkane, reaching 61.6%. However, no CAT activity was detected in CKC-11, and CKC-11 could not grow on alkane. These results indicate that inhibition of beta-oxidation via reconstruction of the transportation process between organelles can facilitate DCA production, but that totally blocking the & betagr;-oxidation would be harmful for energy supply. We thus provide a novel insight into regulation of the beta-oxidation system and metabolic flux. Further understanding of beta-oxidation and the acetyl-CoA transportation system in Candida tropicalis is reached through examination of fermentation data by metabolic flux analysis.
64Cu-Labeled Tetrameric and Octameric RGD Peptides for Small-Animal PET of Tumor v 3 Integrin Expression (2007)

Polyvalency has a profound effect on the receptor-binding affinity and in vivo kinetics of radiolabeled RGD multimers. The information obtained here may guide the future development of RGD peptide-based imaging and internal radiotherapeutic agents targeting integrin alpha(v)beta(3).
Prevention of rhinovirus and poliovirus uncoating by WIN 51711, a new antiviral drug (1986)

WIN 51711, a potent new antipicornavirus drug, has been shown to inhibit an early event in the replication cycle of human poliovirus type 2 and human rhinovirus type 2. WIN 51711 was not virucidal and had no measurable effect on the adsorption of [3H]uridine-labeled virions to cells. When virion penetration of the plasma membrane was determined through loss of sensitivity to neutralizing antisera, WIN 51711 had no effect on poliovirus penetration, but inhibited rhinovirus penetration by 40%. In the presence of WIN 51711, exposure of neutral red-encapsidated virus-infected cells to light at 3 h postinfection resulted in a 3-log reduction in the number of infectious centers, indicating that WIN 51711 maintained the viral RNA in the encapsidated state after penetrating the cell membrane. The inhibition of uncoating by WIN 51711 in the neutral red assay was found to be concentration dependent, with a concentration of 0.03 micrograms/ml resulting in a 90% inhibition of uncoating. Sucrose gradient sedimentation of lysates from whole cells infected with [3H]uridine-labeled poliovirus showed that poliovirions remained intact in the presence of WIN 51711, but were uncoated in the absence of drug. WIN 51711 also prevented thermal inactivation of poliovirus infectivity, indicating a direct stabilizing effect of this compound on virion capsid conformation.
Directly Coupled HPLC-NMR and Its Application to Drug Metabolism (1997)

(1997). Directly Coupled HPLC-NMR and Its Application to Drug Metabolism. Drug Metabolism Reviews: Vol. 29, No. 3, pp. 705-746.
Human tumor cells synthesize an endothelial cell growth factor that is structurally related to basic fibroblast growth factor. (1986)

A human hepatoma cell line synthesizes, as evidenced by metabolic labeling, an endothelial cell mitogen that is found to be mostly cell associated. The hepatoma-derived growth factor (HDGF) has been purified to homogeneity by a combination of Bio-Rex 70, heparin-Sepharose, and reverse-phase chromatography; it is a cationic polypeptide with a molecular weight of about 18,500-19,000. HDGF is structurally related to basic fibroblast growth factor (FGF). Immunological analysis demonstrates that antiserum prepared against a synthetic peptide corresponding to the amino-terminal sequence of basic FGF cross-reacts with HDGF when analyzed by electrophoretic blotting and by immunoprecipitation. Sequence analysis of tryptic fragments demonstrates that HDGF contains sequences that are homologous to both amino-terminal and carboxyl-terminal sequences of basic FGF.
Self-Folding of Three-Dimensional Hydrogel Microstructures (2005)

This letter describes the fabrication of three-dimensional particulate-like hydrogel microstructures using a combination of soft lithography and volume expansion induced self-folding. Bilayer structures are produced by solvent casting and photocuring of liquid resins. They curl into three-dimensional (3D) structures upon contacting with water due to differential swelling of the two layers. The curvature can be controlled by adjusting the polymer composition of the primary swelling layer. A simple semiempirical mathematical model is used to predict this self-folding behavior. By designing the two-dimensional (2D) shapes of the bilayers, this technique can lead to complicated 3D microstructures.
TheSiderophore Receptor IroN of Extraintestinal Pathogenic Escherichia coli Is a Potential VaccineCandidate (2003)

It would be medically and economically desirable to prevent the millions of annual extraintestinal infections and the thousands of associated deaths due to Escherichia coli. Outer membrane proteins are potential vaccine candidates for the prevention of these infections. This study tested the hypotheses that the siderophore receptor IroN is antigenic and that an IroN-specific antibody response confers protection in vivo. Subcutaneous immunization with denatured IroN resulted in a significant IroN immunoglobulin G (IgG)-specific response in serum (P < 0.0001) but not a systemic or mucosal IroN-specific IgA response. In a mouse model of ascending urinary tract infection, subcutaneous immunization with denatured IroN conferred significant protection against renal (P = 0.0135 and 0.0095 in two independent experiments), but not bladder, infection. These data, together with the previously demonstrated role of IroN in virulence, its expression in human biologic fluids, and its prevalence among extraintestinal pathogenic E. coli strains, support further studies on the role of IroN as a vaccine candidate.
End sequence determination from large insert clones using energy transfer fluorescent primers. (1996)

Genome mapping strategies depend heavily on confirmatory data of several types to establish overlaps between contiguous stretches of cloned DNA derived from genomic regions. One type of ancillary data that can contribute to establishing these overlaps is DNA sequence data derived from the ends of large (> 30 kb) inserts in genomic clones. This type of data can be difficult to obtain routinely, because large clones are often unstable and microgram quantities of highly purified DNA are required in each sequencing reaction to obtain sufficient signal for accurate base calling and maximum read length. Recently, we have been experimenting with methods to consistently obtain up to 800 bases of high-quality sequence data from the ends of large insert clones using ThermoSequenase DNA polymerase and Energy Transfer fluorescent primers. Our experimental approach and results, described in this paper, indicate that routinely obtaining high-quality sequence data from the ends of large insert genomic clones is feasible. Such data can contribute to the assessment of common regions between large insert clones, to the establishment of conservation of synteny between closely related species, and to the detection of additional contiguous clones.
A human CD4- T cell leukemia subclone with contact-dependent helper function (1991)

Helper T lymphocytes provide a contact dependent signal to resting B cells that is required for optimal differentiation into Ig-secreting cells. The surface structure(s) on T cells that mediate helper function have not been identified but are known to be induced by T cell activation. A CD4- subclone of the Jurkat leukemic T cell line (D1.1) was isolated and found to be distinct from CD4+ Jurkat clones and a variety of other T and non-T cell leukemic lines in that coculture of D1.1 with resting B cells induced B cells to specifically express surface CD23 molecules, a marker of B cell activation. Furthermore, Jurkat D1.1 induced B cell proliferation and terminal B cell differentiation into IgG-secreting cells in the presence of T cell-dependent B cell mitogens. Similar to the helper effector function of activated T cells, the effects of Jurkat D1.1 were neither Ag nor MHC restricted. Paraformaldehyde fixed Jurkat D1.1 cells remained competent to activate B cells while D1.1 supernatants and diffusible factors were inactive. The effect of Jurkat D1.1 on B cell activation was distinct from that of rIL-4 and was not inhibited by antibodies to IL-4. Together these observations suggested that surface structures on D1.1 and not secreted factors, mediated contact-dependent helper effector function.
Signaling Vascular Morphogenesis and Maintenance (1997)

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A comparison of anti-HER2 IgA and IgG1 in vivo efficacy is facilitated by high N-glycan sialylation of the IgA (2015)

Monomeric IgA has been proposed as an alternative antibody format for cancer therapy. Here, we present our studies on the production, purification and functional evaluation of anti-HER2 IgA antibodies as anti-cancer agents in comparison to the anti-HER2 IgG1 trastuzumab. MALDI-TOF MS analysis showed profound differences in glycosylation traits across the IgA isotypes and cell lines used for production, including sialylation and linkage thereof, fucosylation (both core and antennary) and the abundance of high-mannose type species. Increases in sialylation proved to positively correlate with in vivo plasma half-lives. The polymerization propensity of anti-HER2 IgA2m2 could be suppressed by an 18-aa deletion of the heavy chain tailpiece - coinciding with the loss of high-mannose type N-glycan species - as well as by 2 cysteine to serine mutations at positions 320 and 480. The HER2 F(ab')2-mediated anti-proliferative effect of the IgA2m1 and IgA2m2 subtypes was similar to IgG1, whereas the IgA1 isotype displayed considerably lower potency and efficacy. The Fc-mediated induction of antibody-dependent cell-mediated cytotoxicity (ADCC) using human whole blood ADCC assays did not demonstrate such clear differences between the IgA isotypes. However, the potency of the anti-HER2 IgA antibodies in these ADCC assays was found to be significantly lower than that of trastuzumab. In vivo anti-tumor activity of the anti-HER2 IgA antibodies was compared to that of trastuzumab in a BT-474 breast cancer xenograft model. Multiple dosing and sialylation of the IgA antibodies compensated for the short in vivo half-life of native IgA antibodies in mice compared to a single dose of IgG1. In the case of the IgA2m2 antibody, the resulting high plasma exposure levels were sufficient to cause clear tumor stasis comparable to that observed for trastuzumab at much lower plasma exposure levels.
An Ancient Pathway Combining Carbon Dioxide Fixation with the Generation and Utilization of a Sodium Ion Gradient for ATP Synthesis (2012)

Synthesis of acetate from carbon dioxide and molecular hydrogen is considered to be the first carbon assimilation pathway on earth. It combines carbon dioxide fixation into acetyl-CoA with the production of ATP via an energized cell membrane. How the pathway is coupled with the net synthesis of ATP has been an enigma. The anaerobic, acetogenic bacterium Acetobacterium woodii uses an ancient version of this pathway without cytochromes and quinones. It generates a sodium ion potential across the cell membrane by the sodium-motive ferredoxin:NAD oxidoreductase (Rnf). The genome sequence of A. woodii solves the enigma: it uncovers Rnf as the only ion-motive enzyme coupled to the pathway and unravels a metabolism designed to produce reduced ferredoxin and overcome energetic barriers by virtue of electron-bifurcating, soluble enzymes.
Subepidermal moisture detection of pressure induced tissue damage on the trunk: The pressure ulcer detection study outcomes (2017)

We examined the relationship between subepidermal moisture measured using surface electrical capacitance and visual skin assessment of pressure ulcers at the trunk location (sacral, ischial tuberosities) in 417 nursing home residents residing in 19 facilities. Participants were on average older (mean age of 77 years), 58% were female, over half were ethnic minorities (29% African American, 12% Asian American, and 21% Hispanic), and at risk for pressure ulcers (mean score for Braden Scale for Predicting Pressure Ulcer Risk of 15.6). Concurrent visual assessments and subepidermal moisture were obtained at the sacrum and right and left ischium weekly for 16 weeks. Visual assessment was categorized as normal, erythema, stage 1 pressure ulcer, Deep Tissue Injury or stage 2+ pressure ulcer using the National Pressure Ulcer Advisory Panel 2009 classification system. Incidence of any skin damage was 52%. Subepidermal moisture was measured with a dermal phase meter where higher readings indicate greater moisture (range: 0-70 tissue dielectric constant), with values increasing significantly with the presence of skin damage. Elevated subepidermal moisture values co-occurred with concurrent skin damage in generalized multinomial logistic models (to control for repeated observations) at the sacrum, adjusting for age and risk. Higher subepidermal moisture values were associated with visual damage 1 week later using similar models. Threshold values for subepidermal moisture were compared to visual ratings to predict skin damage 1 week later. Subepidermal moisture of 39 tissue dielectric constant units predicted 41% of future skin damage while visual ratings predicted 27%. Thus, this method of detecting early skin damage holds promise for clinicians, especially as it is objective and equally valid for all groups of patients.
High serum colony-stimulating activity of leukocytopenic patients after intravenous infusions of human urinary colony-stimulating factor (1983)

Eight adult patients suffering from leukocytopenia have been injected by droplet intravenous infusions with partially purified human urinary colony-stimulating factor (CSFHU), which stimulated human monocytes to produce colony-stimulating activity (CSA) in vitro. Three of eight patients were injected with low-dose CSFHU and five with high-dose CSFHU. The infusion of high-dose CSFHU led to a slightly earlier rise in absolute neutrophil counts and a higher CSA level in the serum, as compared to noninjected leukocytopenic patients. There was little toxicity associated with it. Human urinary colony-stimulating factor used in the clinical studies did not have any CSA in vitro in the presence or absence of the patients' sera. These data may suggest that the intravenous infusion of CSFHU increased the serum CSA level, probably through the stimulation of CSA-producing cells in vivo.
Hemolytic-uremic syndrome following bone marrow transplantation in adults for hematologic malignancies (1991)

Abstract One hundred and sixty eight adult patients with B-cell non-Hodgkin's lymphoma (NHL) and other hematologic malignancies who underwent autologous or allogeneic bone marrow transplantation (BMT) were investigated for the subsequent development of hemolytic-uremic syndrome (HUS). All patients were conditioned with cyclophosphamide and total body irradiation. When examined at 3-month intervals for the first year post-BMT, all patients had uniform measurements of hematocrit (Hct) and serum creatinine. Sixteen patients who initially exhibited Hct and creatinine values that were normal range for the BMT populations developed a sudden decrease in Hct and increase in creatinine between 3 and 11 months post-BMT and fulfilled the clinical and laboratory criteria for HUS. None of these patients had known active cytomegalovirus infection, graft-versus-host disease, or cyclosporine administration. The degree of decrease in Hct and creatinine elevation ranged from solely laboratory abnormalities to a clinically significant syndrome. Twelve of the 16 patients developed acute clinical complications of congestive heart failure, hypertension (HTN), or peripheral edema. Twelve patients required red blood cell support, whereas only four patients required platelet transfusions. Both hemolytic anemia and thrombocytopenia have resolved in virtually all cases. At a mean follow up of 18 months postdiagnosis, creatinine elevations have persisted along with HTN. All patients have survived without life-threatening long-term sequelae. With the increasing use of BMT as a curative modality for patients with hematologic malignancies, it becomes important to prospectively monitor patients for the development of HUS and its potential long-term impact on renal function.
The quest for mammalian Polycomb response elements: are we there yet? (2015)

A long-standing mystery in the field of Polycomb and Trithorax regulation is how these proteins, which are highly conserved between flies and mammals, can regulate several hundred equally highly conserved target genes, but recognise these targets via cis-regulatory elements that appear to show no conservation in their DNA sequence. These elements, termed Polycomb/Trithorax response elements (PRE/TREs or PREs), are relatively well characterised in flies, but their mammalian counterparts have proved to be extremely difficult to identify. Recent progress in this endeavour has generated a wealth of data and raised several intriguing questions. Here, we ask why and to what extent mammalian PREs are so different to those of the fly. We review recent advances, evaluate current models and identify open questions in the quest for mammalian PREs.
Selenium-induced inhibition of angiogenesis in mammary cancer at chemopreventive levels of intake (1999)

The trace element nutrient selenium (Se) has been shown to possess cancer-preventive activity in both animal models and humans, but the mechanisms by which this occurs remain to be elucidated. Because angiogenesis is obligatory for the genesis and growth of solid cancers, we investigated, in the study presented here, the hypothesis that Se may exert its cancer-preventive activity, at least in part, by inhibiting cancer-associated angiogenesis. The effects of chemopreventive levels of Se on the intra-tumoral microvessel density and the expression of vascular endothelial growth factor in 1-methyl-1-nitrosourea-induced rat mammary carcinomas and on the proliferation and survival and matrix metalloproteinase activity of human umbilical vein endothelial cells in vitro were examined. Increased Se intake as Se-enriched garlic, sodium selenite, or Se-methylselenocysteine led to a significant reduction of intra-tumoral microvessel density in mammary carcinomas, irrespective of the manner by which Se was provided: continuous exposure (7-wk feeding) with a chemoprevention protocol or acute bolus exposure (3 d) after carcinomas had established. Compared with the untreated controls, significantly lower levels of vascular endothelial growth factor expression were observed in a sizeable proportion of the Se-treated carcinomas. In contrast to the mammary carcinomas, the microvessel density of the uninvolved mammary glands was not altered by Se treatment. In cell culture, direct exposure of human umbilical vein endothelial cells to Se induced cell death predominantly through apoptosis, decreased the gelatinolytic activities of matrix metalloproteinase-2, or both. These results indicate a potential for Se metabolites to inhibit key attributes (proliferation, survival, and matrix degradation) of endothelial cells critical for angiogenic sprouting. Therefore, inhibition of angiogenesis associated with cancer may be a novel mechanism for the anticancer activity of Se in vivo, and multiple mechanisms are probably involved in mediating the anti-angiogenic activity.
Antioxidant Activity of Prune (Prunus domestica L.) Constituents and a New Synergist (2002)

Ethanol extract of prune was separated into hexane-soluble and H(2)O-soluble fractions, and the H(2)O-soluble fraction was further separated into a methanol (MeOH) eluate and an H(2)O eluate by Diaion HP-20 column chromatography. The MeOH eluate exhibited the strongest antioxidant activity among the separated fractions evaluated by oxygen radical absorbance capacity (ORAC). Further purification of the MeOH eluate led to isolation of a novel compound, 4-amino-4-carboxychroman-2-one, together with four known compounds (p-coumaric acid, vanillic acid beta-glucoside, protocatechuic acid, and caffeic acid), structures of which were identified by NMR and MS analyses. The ORAC values of these isolated compounds showed 0.15-1.43 units (micromol of Trolox equiv)/micromol, and the new compound showed a remarkable synergistic effect on caffeoylquinic acid isomers. The antioxidant activity of the MeOH eluate was highly dependent on the major prune components, caffeoylquinic acid isomers, with a contribution from the new synergist.
Caffeine for asthma (2001)

Caffeine appears to improve airways function modestly in people with asthma for up to four hours. People may need to avoid caffeine for at least four hours prior to lung function testing.
More than third of world's population has been infected with hepatitis B virus (1999)

EDITOR—The news items on the prevalence of hepatitis B infection is incorrect and the accompanying artificially coloured photograph is misleading.1 Electron micrographs are usually negatively stained (figure).



Electron micrograph of hepatitis B virus (double shelled particle) and excess surface antigen protein (tubular forms and small spherical particles) (magnification ×252 000)



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