gebhart/patrepeval huggingface dataset:
Effect of inulin on the human gut microbiota: stimulation ofBifidobacterium adolescentisandFaecalibacterium prausnitzii (2008)

Prebiotics are food ingredients that improve health by modulating the colonic microbiota. The bifidogenic effect of the prebiotic inulin is well established; however, it remains unclear which species of Bifidobacterium are stimulated in vivo and whether bacterial groups other than lactic acid bacteria are affected by inulin consumption. Changes in the faecal microbiota composition were examined by real-time PCR in twelve human volunteers after ingestion of inulin (10 g/d) for a 16-d period in comparison with a control period without any supplement intake. The prevalence of most bacterial groups examined did not change after inulin intake, although the low G+C % Gram-positive species Faecalibacterium prausnitzii exhibited a significant increase (10.3% for control period v. 14.5% during inulin intake, P=0.019). The composition of the genus Bifidobacterium was studied in four of the volunteers by clone library analysis. Between three and five Bifidobacterium spp. were found in each volunteer. Bifidobacterium adolescentis and Bifidobacterium longum were present in all volunteers, and Bifidobacterium pseudocatenulatum, Bifidobacterium animalis, Bifidobacterium bifidum and Bifidobacterium dentium were also detected. Real-time PCR was employed to quantify the four most prevalent Bifidobacterium spp., B. adolescentis, B. longum, B. pseudocatenulatum and B. bifidum, in ten volunteers carrying detectable levels of bifidobacteria. B. adolescentis showed the strongest response to inulin consumption, increasing from 0.89 to 3.9% of the total microbiota (P=0.001). B. bifidum was increased from 0.22 to 0.63% (P<0.001) for the five volunteers for whom this species was present.
The Action of α‐Mannosidase from Oerskovia sp. on the Mannose‐Rich O‐Linked Sugar Chains of Glycoproteins (1997)

Alpha-mannosidase was isolated from the culture liquid of Oerskovia sp. The purified enzyme had a molecular mass of 480 kDa and comprises four identical subunits. The enzyme cleaves bonds in side chains of yeast mannan (Km = 0.08 mM, k(cat) = 1.02 micromol x min(-1) x mg(-1)) and reveals a low activity towards p-nitrophenyl alpha-D-mannopyranoside. The alpha-mannosidase is a Ca2+-dependent enzyme and is inhibited by EDTA. The enzyme possess no endo-mannosidase activity releasing only mannose in the reaction with the inversion of anomeric configuration and could be classified as exo-alpha-mannanase. The enzyme revealed a high deglycosylating activity towards the short mannose-rich O-linked carbohydrate chains of glycoproteins.
Cyclic amidines. Part XXII. Novel isomerism of disubstituted tricycloquinazolines and molecular orientations in carcinogenesis (1970)

Certain disubstituted tricycloquinazolines exhibit an unusual structural isomerism originating from the modification of the symmetry of tricycloquinazoline by substitution. Molecular orientations specific for carcinogenesis, consistent with differences in the carcinogenic activities of such isomers and other 2-substituted tricycloquinazolines, have been deduced.
Imidazo[4,5-c]pyridines (3-deazapurines) and their nucleosides as immunosuppressive and antiinflammatory agents (1986)

A variety of imidazo[4,5-c]pyridines (3-deazapurines) were synthesized. With use of these aglycons as pentosyl acceptors, the corresponding ribonucleosides and 2'-deoxyribonucleosides were prepared by an enzymatic method involving transfer of the pentosyl moiety from appropriate pyrimidine nucleosides. With most of the imidazo[4,5-c]pyridines, the products obtained from the enzyme-catalyzed reactions were pentosylated exclusively in the 1-position. However, some 3-pentosylation occurred with aglycons that had H or N3 in the 4-position. In addition to the 2'-deoxy congener of the ribonucleoside of 4-amino-1H-imidazo[4,5-c]pyridine, the 5'-deoxy and 2',5'-dideoxy congeners were synthesized. All of the aglycons and their nucleosides were tested for toxicity to mammalian cells in culture. None were markedly cytotoxic. These compounds were also evaluated for their ability to inhibit lymphocyte-mediated cytolysis in vitro. 3-Deazaadenosine (23) and its 2'-deoxy congener (38) were the most potent inhibitors (ED50 = 20 microM). In addition to these two in vitro tests, in vivo inhibition of the inflammatory response in the rat carregeenan pleurisy model was determined. 3-Deazaadenosine (23) was the most potent compound (ED50 = 3 mg/kg) in this in vivo test.
Inhibition of Pro‐Inflammatory Functions of Human Neutrophils by Constituents of Melodorum fruticosum Leaves (2018)

In an initial screening, the dichloromethane extract from the leaves of Melodorum fruticosum showed distinct inhibitory effects on the release of interleukin-8 (IL-8) in human neutrophils. Therefore, the aim of the present study was the phytochemical and pharmacological investigation of this extract, to better understand which compounds might be responsible for the anti-inflammatory effect. Phytochemical analysis led to the isolation of 12 known compounds and two new natural products, 5-hydroxy-6-(2-hydroxybenzyl)-4',7-dimethoxyflavanone (13) and 2',4'-dihydroxy-3'-(2-hydroxybenzyl)-4,6'-dimethoxychalcone (14). The influence of the isolated compounds on the production and release of the pro-inflammatory factors IL-8, tumor necrosis factor alpha (TNF-α), reactive oxygen species (ROS), and adhesion molecules (CD62L and CD11b) in human neutrophils was evaluated. Three constituents, melodamide A, 2',4'-dihydroxy-4,6'-dimethoxychalcone, and 2',6'-dihydroxy-4'-methoxychalcone, showed significant inhibition of IL-8 release (IC<sub>50</sub> =6.6, 8.6, and 11.6 μm, respectively) and TNF-α production (IC<sub>50</sub> =4.5, 13.3, and 6.2 μm, respectively).
Induction of microglial apoptosis by corticotropin‐releasing hormone (2006)

Neuropeptides are short-chain peptides found in brain tissue, some of which function as neurotransmitters and others as hormones. Neuropeptides may directly or indirectly modulate glial functions in the CNS. In the present study, effects of various neuropeptides on the viability and inflammatory activation of cultured microglia were investigated. Vasoactive intestinal peptide, substance P, cholecystokinin and neuropeptide Y did not affect microglial cell viability, whereas corticotropin-releasing hormone (CRH) induced a classical apoptosis of mouse microglia in culture as shown by nuclear condensation and fragmentation, terminal deoxynucleotidyl transferase dUTP nick-end labeling, and cleavage of caspase 3 and poly(ADP-ribose) polymerase protein. CRH, however, did not influence nitric oxide production or expression of inflammatory genes including those encoding cytokines and chemokines, indicating that CRH did not affect the inflammatory activation of microglia. The CRH-induced microglial apoptosis appeared to involve a mitochondrial pathway and reactive oxygen species, based on the mitochondrial membrane potential change, caspase 9 activation and sensitivity to antioxidants. Taken together, our results indicate that the stress neuropeptide CRH may regulate neuroinflammation by inducing the apoptosis of microglia, the major cellular source of inflammatory mediators in the CNS.
Graphite Oxide:  Chemical Reduction to Graphite and Surface Modification with Primary Aliphatic Amines and Amino Acids (2003)

The chemical reduction of graphite oxide (GO) to graphite by either NaBH4 or hydroquinone and also its surface modification with neutral, primary aliphatic amines and amino acids are described. Treatment of GO with NaBH4 leads to turbostatic graphite that upon calcination under an inert atmosphere is transformed to highly ordered graphitic carbon, while the reduction with hydroquinone yields directly crystalline graphite under soft thermal conditions. On account of the surface-exposed epoxy groups present in the GO solid, its surface modification with neutral, primary aliphatic amines or amine-containing molecules (amino acids and aminosiloxanes) takes place easily through the corresponding nucleophilic substitution reactions. In this way, valuable GO derivatives can be obtained, like molecular pillared GO, organically modified GO affording in organic solvents stable organosols or hydrophilic GO affording in water stable hydrosols and possessing direct cation exchange sites. The potential combination of surface modification and chemical reduction of GO in producing novel graphite based materials is also presented.
ChemInform Abstract: Rapid Method for the Functionalization of Polymer Supports for Solid Phase Oligonucleotide Synthesis. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Intracellular processing of the Newcastle disease virus fusion glycoprotein (1985)

The fusion glycoprotein (Fo) of Newcastle disease virus is cleaved at an intracellular site (Nagai et al., Virology 69:523-538, 1976) into F1 and F2. This result was confirmed by comparing the transit time of the fusion protein to the cell surface with the time course of cleavage of Fo. The time required for cleavage of half of the pulse-labeled Fo protein is ca. 40 min faster than the half time of the transit of the fusion protein to the cell surface. To determine the cell compartment in which cleavage occurs, use was made of inhibitors which block glycoprotein migration at specific points and posttranslational modifications known to occur in specific cell membranes. Cleavage of Fo is inhibited by carbonyl cyanide m-chlorophenylhydrazone; thus, cleavage does not occur in the rough endoplasmic reticulum. Monensin blocks the incorporation of Newcastle disease virus glycoproteins into virions and blocks the cleavage of the fusion glycoprotein. However, Fo cannot be radioactively labeled with [3H] fucose, whereas F1 is readily labeled. These results argue that cleavage occurs in the trans Golgi membranes or in a cell compartment occupied by glycoproteins quite soon after their transit through the trans Golgi membranes. The implications of the results presented for the transit times of the fusion protein between subcellular organelles are discussed.
Curriculum learning (2009)

Humans and animals learn much better when the examples are not randomly presented but organized in a meaningful order which illustrates gradually more concepts, and gradually more complex ones. Here, we formalize such training strategies in the context of machine learning, and call them "curriculum learning". In the context of recent research studying the difficulty of training in the presence of non-convex training criteria (for deep deterministic and stochastic neural networks), we explore curriculum learning in various set-ups. The experiments show that significant improvements in generalization can be achieved. We hypothesize that curriculum learning has both an effect on the speed of convergence of the training process to a minimum and, in the case of non-convex criteria, on the quality of the local minima obtained: curriculum learning can be seen as a particular form of continuation method (a general strategy for global optimization of non-convex functions).
Distribution and molecular characterization of a cell‐surface and a cytoplasmic antigen detectable in human melanoma cells with monoclonal antibodies (1981)

The monoclonal antibodies 225.28S and 465.12 to human melanoma-associated antigens have been tested with a large variety of surgically removed skin lesions and malignant tumors as well as with a panel of cultured cell lines in serological and immunochemical assays. The antibody 225.28S reacts with a plasma membrane antigen while the antibody 465.12 detects a cytoplasmic antigen. Both antibodies fail to react with melanocytes from normal skin as well as benign skin lesions but react with nevi, melanoma cells and some skin carcinomas. Analysis with surgically removed tumors and cultured human cell lines indicated that the plasma membrane antigen is restricted to skin lesions whereas the cytoplasmic antigen is synthesized by tumor cells of various histological origins. The plasma membrane antigen is composed of two glyco-polypeptides of 280,000 and greater than 440,000 daltons, while the cytoplasmic antigen consists of 4 glycopolypeptides of 94,000, 75,000, 70,000 and 25,000 daltons. None of these components are bridged by disulfide bonds. The cytoplasmic antigen was readily detected in the spent culture medium of melanoma cell lines in the form of a major 94,000 dalton and a minor 72,000 dalton structure, while the plasma membrane antigen was detectable only after vastly increasing the sensitivity of the assay system.
Asialoglycoprotein receptor deficiency in mice lacking the minor receptor subunit. (1994)

The asialoglycoprotein receptor is an abundant heterooligomeric endocytic receptor that is predominantly expressed on the sinusoidal surface of the hepatocytes. Proposed physiological and pathophysiological functions ascribed to this hepatic lectin (HL) include the removal of desialylated serum glycoproteins and apoptotic cells, clearance of chylomicron remnants, and a role as a homing receptor for lymphatic and metastatic cells. The assembly of two homologous subunits, HL-1 and HL-2, is required to form functional, high affinity receptors on the cell surface. However, the importance of the individual subunits for receptor transport to the cell surface has been controversial. To explore the significance of the minor HL-2 subunit for receptor expression and function in vivo, we have disrupted the HL-2 gene in mice. Homozygous HL-2-deficient animals are superficially normal. However, HL-1 expression in the liver is greatly reduced, indicating that HL-2 may promote HL-1 stability. Although these mice are completely unable to clear asialoorosomucoid, a high affinity ligand for asialoglycoprotein receptor, they do not accumulate desialylated glycoproteins or lipoproteins in their circulation.
Phase II Study of Low-Dose Decitabine in Patients With Chronic Myelogenous Leukemia Resistant to Imatinib Mesylate (2005)

Decitabine induces hypomethylation and has clinical activity in imatinib refractory chronic myelogenous leukemia. We hypothesize that the inverse correlation between hypomethylation 2 weeks after therapy and response is due to a cell death mechanism of response, whereby resistant cells can withstand more hypomethylation.
Quantification of Oligonucleotides by LC–MS/MS: The Challenges of Quantifying A Phosphorothioate Oligonucleotide and Multiple Metabolites (2014)

We show that quantification of an oligonucleotide and multiple metabolites, including isobaric 3´ and 5´ metabolites, is achievable in a single assay through good sample clean-up and careful optimization of the LC-MS/MS parameters. The strategy presented here can be applied elsewhere and may be useful for other oligonucleotides and their metabolites.
Noninvasive Blood Glucose Assay by Near-Infrared Diffuse Reflectance Spectroscopy of the Human Inner Lip (1993)

Near-infrared (NIR) spectra of the human inner lip were obtained by using a special optimized accessory for diffuse reflectance measurements. The partial-least squares (PLS) multivariate calibration algorithm was applied for linear regression of the spectral data between 9000 and 5500 cm −1 (Λ = 1.1–1.8 μm) against blood glucose concentrations determined by a standard clinical enzymatic method. Calibration experiments with a single person were carried out under varying conditions, as well as with a population of 133 different patients, with capillary and venous blood glucose concentration values provided. A genuine correlation between the blood glucose concentrations and the NIR-spectra can be proven. A time lag of about 10 min for the glucose concentration in the spectroscopically probed tissue volume vs. the capillary concentration can be estimated. Mean-square prediction errors obtained by cross-validation were in the range of 45 to 55 mg/dL. An analysis of different variance factors showed that the major contribution to the average prediction uncertainty was due to the reduced measurement reproducibility, i.e., variations in lip position and contact pressure. The results demonstrate the feasibility of using diffuse reflectance NIR-spectroscopy for the noninvasive measurement of blood glucose.
Antigenic and molecular characterization of host cell-mediated variants of equine H3N8 influenza viruses (1994)

Antigenic differences between three of six equine influenza virus (H3N8) MDCK cell- and egg-derived pairs have been demonstrated using monoclonal and polyclonal antibodies. Sequencing of the haemagglutinin (HA) genes revealed amino acid changes in four of the six virus pairs. These data contrast with those for human isolates of influenza virus in that it was predominantly tissue culture-isolated equine virus and not egg-derived virus which displayed heterogeneity. Some of the molecular changes involved are located within the vicinity of the cell receptor-binding site (positions 156, 158 and 222) whereas others are in the vicinity of the HA1-HA2 cleavage site (positions 18 and 32 of HA1 and position 12 of HA2). Our results indicate that the host cell can play a part in selecting antigenic variants of equine influenza virus and suggest that the egg, and not cell culture as is the case for human isolates, is the preferred host for vaccine and antigenic studies.
Implausibility of an aetiological association between cytomegalovirus and Kaposi's sarcoma shown by four techniques. (1989)

The presence of cytomegalovirus (CMV) was analysed in either lymph node or skin and lung tissue necropsy specimens affected by Kaposi's sarcoma, from 10 patients who had died of AIDS. The different detection techniques used were: (i) immunohistochemical demonstration of CMV immediate early antigen (IEA); (ii) in situ hybridisation with a biotinylated CMV DNA probe; (iii) Southern blot hybridisation of DNA extracted from sequential tissue sections; and (iv) polymerase chain reaction (PCR) with CMV specific primers on the DNA samples. The results of these analyses were compared with the postmortem data on CMV obtained by infectious particle assays and histological examination, especially of adrenal glands of the same patients. The results of the various detection methods correlated very well, yielding a combined score of six of 10 patients positive for CMV; there did not seem to be any association between the presence of CMV and the occurrence of Kaposi's sarcoma in our patients.
MeDIP real‐time qPCR of maternal peripheral blood reliably identifies trisomy 21 (2012)

The MeDIP real-time qPCR method for noninvasive prenatal diagnosis of trisomy 21 was confirmed and revalidated in 175 samples with satisfactory results demonstrating that it is accurate and reproducible. We are currently working towards simplification of the method to make it more robust and therefore easily, accurately, and rapidly reproduced and adopted by other laboratories. Nevertheless, larger scale validation studies are necessary before the MeDIP real-time qPCR-based method could be applied in clinical practice.
Biomass combustion: Relationship between pollutant formation and fuel composition (1989)

A 65-kW refractory-walled reactor was used to study biomass combustion under conditions typical of the suspension-burning phase in a spreader-stoker-fired boiler. Isothermal combustion data and nitric oxide (NO) emission rates were obtained as a function of temperature, local oxygen concentration, and vertical velocity for sized biomass fuels. Two softwoods, a hardwood, and a North Carolina peat were studied
Immunohistochemical Detection of EGFRvIII in High Malignancy Grade Astrocytomas and Evaluation of Prognostic Significance (2004)

The purpose of this study was to establish an accurate and accessible immunohistochemical (IHC) method for detecting vIII Egf receptor and to assess the prognostic significance of the method as applied to the detection of vIII in malignant astrocytomas. The accuracy of the method was determined by comparing vIII immunoreactivity in formalin-fixed and paraffin-embedded tumor sections versus RT-PCR results from the analysis of RNA extracted from corresponding frozen specimens. RT-PCR revealed vIII transcript in 18 of 44 cases in this series, and IHC analysis of matched formalin-fixed and paraffin-embedded sections showed EGFRvIII reactivity in each of these 18 tumors, as well as 1 additional tumor that was negative for vIII transcript. EGFR amplification was evident in all tumors expressing vIII; none of the 15 tumors lacking amplified EGFR were positive for vIII transcript or vIII protein. IHC analysis for vill expression was next applied to a large series of anaplastic astrocytomas (AAs) and glioblastoma multiforme (GBMs) from clinical trial patients with complete follow-up and that had been previously examined by FISH for amplified EGFR. Among the GBMs, vIII detection by IHC was determined in 19 of 46 cases (41.3%) with EGFR amplification, and in only 3 of 59 tumors lacking amplified EGFR (5.1%). Among the AAs, vIII expression was observed in 3 of 14 cases with amplified EGFR (21.4%) and in 6 of 49 cases without EGFR amplification (12.2%). GBM and AA patient survival analysis as a function of vIII expression showed contrasting results, with vIII positivity having no association with survival among GBM patients (p = 0.84), but being highly associated with reduced survival among AA patients (p = 0.0016). This latter finding, though quite possibly a result of vIII's association with increasing AA patient age, suggests that vIII IHC will be useful for identifying and/or confirming the identity of malignant astrocytomas whose clinical behavior is consistent with that of GBM.
Cholera Toxin B: One Subunit with Many Pharmaceutical Applications (2015)

Cholera, a waterborne acute diarrheal disease caused by Vibrio cholerae, remains prevalent in underdeveloped countries and is a serious health threat to those living in unsanitary conditions. The major virulence factor is cholera toxin (CT), which consists of two subunits: the A subunit (CTA) and the B subunit (CTB). CTB is a 55 kD homopentameric, non-toxic protein binding to the GM1 ganglioside on mammalian cells with high affinity. Currently, recombinantly produced CTB is used as a component of an internationally licensed oral cholera vaccine, as the protein induces potent humoral immunity that can neutralize CT in the gut. Additionally, recent studies have revealed that CTB administration leads to the induction of anti-inflammatory mechanisms in vivo. This review will cover the potential of CTB as an immunomodulatory and anti-inflammatory agent. We will also summarize various recombinant expression systems available for recombinant CTB bioproduction.
Isolation, characterization, and physiological role of the pyruvate dehydrogenase complex and alpha-acetolactate synthase of Lactococcus lactis subsp. lactis bv. diacetylactis (1992)

The pyruvate dehydrogenase complex of Lactococcus lactis subsp. lactis bv. diacetylactis has a specific activity of 6.6 U/mg and a Km of 1 mM for pyruvate. The specific activities of E2 and E3 in the complex are 30 and 0.36 U/mg, respectively. The complex is very sensitive to NADH inhibition and consists of four subunits: E1 alpha (44 kDa), E1 beta (35 kDa), E2 (73 kDa), and E3 (60 kDa). The L. lactis alpha-acetolactate synthase has a specific activity of 103 U/mg and a Km of 50 mM for pyruvate. Thiamine pyrophosphate (Km = 3.2 microM) and divalent cations are essential for activity. The native enzyme measures 172 kDa and consists of 62-kDa monomers. The role of both enzymes in product formation is discussed in view of NADH inhibition and competition for pyruvate.