gebhart/patrepeval huggingface dataset:
In VitroCulture Conditions for Maintaining a Complex Population of Human Gastrointestinal Tract Microbiota (2011)

A stable intestinal microbiota is important in maintaining human physiology and health. Although there have been a number of studies using in vitro and in vivo approaches to determine the impact of diet and xenobiotics on intestinal microbiota, there is no consensus for the best in vitro culture conditions for growth of the human gastrointestinal microbiota. To investigate the dynamics and activities of intestinal microbiota, it is important for the culture conditions to support the growth of a wide range of intestinal bacteria and maintain a complex microbial community representative of the human gastrointestinal tract. Here, we compared the bacterial community in three culture media: brain heart infusion broth and high- and low-carbohydrate medium with different growth supplements. The bacterial community was analyzed using denaturing gradient gel electrophoresis (DGGE), pyrosequencing and real-time PCR. Based on the molecular analysis, this study indicated that the 3% fecal inoculum in low-concentration carbohydrate medium with 1% autoclaved fecal supernatant provided enhanced growth conditions to conduct in vitro studies representative of the human intestinal microbiota.
Iterative In Situ Click Chemistry Creates Antibody‐like Protein‐Capture Agents (2009)

Special agents for protein capture: Iterative in situ click chemistry (see scheme for the tertiary ligand screen) and the one-bead-one-compound method for the creation of a peptide library enable the fragment-based assembly of selective high-affinity protein-capture agents. The resulting ligands are water-soluble and stable chemically, biochemically, and thermally. They can be produced in gram quantities through copper(I)-catalyzed cycloaddition.
Opsonic recognition of staphylococci mediated by cell wall peptidoglycan: antibody-independent activation of human complement and opsonic activity of peptidoglycan antibodies. (1980)

Abstract In an effort to determine the cell surface component(s) of importance in the opsonic recognition of staphylococci, the interactions of intact bacterial cells, isolated cell walls, and purified cell wall components with human complement (C) and immunoglobulins were investigated. Intact cells of five strains of Staphylococcus aureus and one strain of Staphylococcus epidermidis were found to consume human C via both the classical and the alternative pathway. Activation of C resulted in the deposition of opsonically active C3 molecules on the surface of the staphylococci. All cell wall components contributed to the consumption of C via the antibody-dependent classical pathway. Activation of the alternative C pathway, however, was mediated exclusively by the pepti-doglycan moiety of the staphylococcal cell wall. The other major cell wall components, teichoic acid, lipotei-choic acid, and protein A, were without effect on the alternative pathway. Staphylococcal opsonization in human agammaglobulinemic serum (immunoglobulins ≃ 0.5% of normal) was also mediated by peptidoglycan and involved activation of the alternative C pathway. Kinetic studies revealed that C activation, C3 fixation, and opsonization proceeded at a slower rate via the alternative pathway than when both pathways were used. Optimal opsonization of staphylococci, therefore, requires immunoglobulins as well as an intact classical pathway. The capacity of peptidoglycan to absorb heat-stable opsonins from immune serum and the ability of the eluted peptidoglycan antibody to promote phagocytosis of staphylococci by human polymorphonuclear leukocytes provide further evidence for the key role of peptidoglycan in the opsonic recognition of staphylococci by the human host, and it is suggested that this may be true for other Gram-positive bacterial species as well.
Presence and Function of the Calcitonin Gene-Related Peptide Receptor on Rat Pial Arteries Investigated In Vitro and In Vivo (2005)

Calcitonin gene-related peptide (CGRP) and related peptides may be involved in migraine pathogenesis. To understand their vasomotor role in the cerebral circulation, we performed two studies, a pressurized arteriography study of the middle cerebral artery (MCA) and a genuine closed cranial window (gCCW) in vivo study. Using the pressurized arteriography model rat MCAs were mounted on micropipettes, pressurized to 85 mmHg and luminally perfused. The diameter responses to luminally and abluminally applied rat-alphaCGRP, rat-betaCGRP, amylin and adrenomedullin were compared with the resting diameter. Only abluminally applied CGRP induced dilation of the cerebral arteries; E(max) for alphaCGRP and betaCGRP were 35 +/- 0.5% and 10.8 +/- 0.2%. These responses were blocked by CGRP(8-37). The gCCW model allowed videomicroscopic visualization of the pial vessels in anaesthetized rats. Changes in vessel diameter to intravenously administered alphaCGRP and betaCGRP were compared with pre-infusion baseline. Intravenous infusion of alphaCGRP and betaCGRP in the highest dose induced dilation of the cerebral cortical pial arteries/arterioles of 40.3 +/- 7.5% and 49.1 +/- 8.4%, respectively. However, this was probably secondary to a decrease in blood pressure of 44.8 +/- 3.3 mmHg and 49.2 +/- 3.3 mmHg. Our results suggest that CGRP receptors are probably functional on the smooth muscle cells and not on the endothelium of rat cerebral arteries.
A computer-assisted system for 3-D frameless localization in stereotaxic MRI (1991)

A low-cost PC-based system for 3-D localization of brain targets in stereotaxic imaging is presented. It relies on a method, using MR images, in which four markers are inserted in the fastenings of a Talairach stereotaxic frame during MRI examination. By locating these markers on the images with this system, the transformation matrixes can be computed to obtain the 3-D coordinates of the center of a tumour in the stereotaxic space or in the MRI space. The system calculates the frame and arc setting parameters of a probe trajectory to the target, either for an orthogonal or a double oblique approach if needed. Simulated probe trajectory intersections with consecutive slices can be viewed in order to validate the trajectory before and during the surgical procedure. The method presents no major constraints in routine examinations. Mathematical details on the calculation of the transformation matrices are given.
Laminin-332-Integrin Interaction: A Target For Cancer Therapy? (2008)

For many years, extracellular matrix (ECM) was considered to function as a tissue support and filler. However, we now know that ECM proteins control many cellular events through their interaction with cell-surface receptors and cytoplasmic signaling pathways. For example, they regulate cell proliferation, cell division, cell adhesion, cell migration, and apoptosis. We focus in this review on a laminin isoform, laminin-332 (formerly termed laminin-5), a major component of the basement membrane (BM) of skin and other epithelial tissues. It is composed of 3 subunits (alpha3beta3 and gamma3 and interacts with at least two integrin receptors expressed by epithelial cells (alpha3beta1 and alpha6beta4 integrin. Mutations in either laminin-332 or integrin alpha6beta4 result in junctional epidermolysis bullosa, a blistering skin disease, while targeting of laminin-332 by autoantibodies in cicatricial pemphigoid leads to dysadhesion of epithelial cells from their underlying connective tissue. Abnormal expression of laminin-332 and its integrin receptors is also a hallmark of certain tumor types and is believed to promote invasion of colon, breast and skin cancer cells. Moreover, there is emerging evidence that laminin-332 and its protease degradation products are not only found at the leading front of several tumors but also likely induce and/or promote tumor cell migration. Thus, in this review, we focus specifically on the role of laminin-332 and its integrin receptors in adhesion, proliferation, and migration/invasion of cancer cells. Finally, we discuss strategies for the development of laminin-332-based antagonists for the treatment of malignant tumors.
Remarkable β-Selectivity in the Synthesis of β-1-C-Arylglucosides:  Stereoselective Reduction of Acetyl-Protected Methyl 1-C-Arylglucosides without Acetoxy-Group Participation (2007)

An efficient and practical process to generate β-C-arylglucoside derivatives was achieved. The process described involves Lewis acid mediated ionic reduction of a peracetylated 1-C-aryl methyl glucoside derived from the addition of an aryl-Li to selectively protected δ-d-gluconolactone. The reduction of the 2-acetoxy-1-C-oxacarbenium ion intermediates proceeds with a high degree of selectivity to give β-C-arylglucosides without 2-acetoxy group participation. Furthermore, during the reduction process we also identified an unprecedented critical role of water. By changing from the usual benzyl ether protecting groups because of cost and chemical compatibility concerns, the new process is made additionally efficient and highly selective.
Functional analysis of the ALG3 gene encoding the Dol-P-Man: Man5GlcNAc2-PP-Dol mannosyltransferase enzyme of P. pastoris (2004)

N-glycans are synthesized in both yeast and mammals through the ordered assembly of a lipid-linked core Glc(3)Man(9)GlcNAc(2) structure that is subsequently transferred to a nascent protein in the endoplasmic reticulum. Once folded, glycoproteins are then shuttled to the Golgi, where additional but divergent processing occurs in mammals and fungi. We cloned the Pichia pastoris homolog of the ALG3 gene, which encodes the enzyme that converts Man(5)GlcNAc(2)-Dol-PP to Man(6)GlcNAc(2)-Dol-PP. Deletion of this gene in an och1 mutant background resulted in the secretion of glycoproteins with a predicted Man(5)GlcNAc(2) structure that could be trimmed to Man(3)GlcNAc(2) by in vitro alpha-1,2-mannosidase treatment. However, several larger glycans ranging from Hex(6)GlcNAc(2) to Hex(12)GlcNAc(2) were also observed that were recalcitrant to an array of mannosidase digests. These results contrast the far simpler glycan profile found in Saccharomyces cerevisiae alg3-1 och1, indicating diverging Golgi processing in these two closely related yeasts. Finally, analysis of the P. pastoris alg3 deletion mutant in the presence and absence of the outer chain initiating Och1p alpha-1,6-mannosyltransferase activity suggests that the PpOch1p has a broader substrate specificity compared to its S. cerevisiae counterpart.
Long-Term Treatment of Alcoholic Liver Disease with Propylthiouracil (1987)

Propylthiouracil has been shown experimentally to protect against alcohol-induced hepatocellular necrosis in hypoxic conditions. An earlier, short-term study of patients with alcoholism and liver disease indicated clinical improvement with propylthiouracil, but the effect on mortality could not be assessed. In the present study, we investigated the effect of propylthiouracil on mortality in patients with alcoholic liver disease in a long-term, double-blind, randomized clinical trial involving 310 compliant patients who received propylthiouracil (n = 157) or placebo (n = 153) for a maximum of two years. There were no differences between the two groups in demographic and clinical characteristics and biopsy-confirmed diagnoses at randomization, or in daily urinary alcohol levels during the study. The cumulative dropout rate over two years was not significantly different (propylthiouracil group, 0.68; placebo group, 0.60). The group receiving propylthiouracil (300 mg per day) had a cumulative mortality rate half that in the group receiving placebo (0.13 vs. 0.25 [P less than 0.05] in the total sample, and 0.25 vs. 0.55 [P less than 0.03] in a subgroup of severely ill patients [propylthiouracil group, n = 56; placebo group, n = 41]). Proportional-hazards stepwise regression analyses indicated that only propylthiouracil treatment, prothrombin time, hemoglobin levels, and mean daily urinary alcohol levels significantly affected mortality. The hazards ratio for the complete group indicated that mortality in the propylthiouracil group was 0.38 (95 percent confidence interval, 0.20 to 0.83) that of the placebo group. Protection by propylthiouracil was not observed in patients with high morning urinary alcohol levels. No clinically important side effects of propylthiouracil were observed at the dose used. We conclude that the administration of propylthiouracil can reduce mortality due to alcoholic liver disease.
Physics of thin-film ferroelectric oxides (2005)

This review covers important advances in recent years in the physics of thin-film ferroelectric oxides, the strongest emphasis being on those aspects particular to ferroelectrics in thin-film form. The authors introduce the current state of development in the application of ferroelectric thin films for electronic devices and discuss the physics relevant for the performance and failure of these devices. Following this the review covers the enormous progress that has been made in the first-principles computational approach to understanding ferroelectrics. The authors then discuss in detail the important role that strain plays in determining the properties of epitaxial thin ferroelectric films. Finally, this review ends with a look at the emerging possibilities for nanoscale ferroelectrics, with particular emphasis on ferroelectrics in nonconventional nanoscale geometries.
Functional analysis of a stable transcription arrest site in the first intron of the murine adenosine deaminase gene. (1993)

Transcription arrest plays a role in regulating the expression of a number of genes, including the murine adenosine deaminase (ADA) gene. We have previously identified two prominent arrest sites at the 5' end of the ADA gene: one in the first exon and one in the first intron (J. W. Innis and R. E. Kellems, Mol. Cell. Biol. 11:5398-5409, 1991). Here we report the functional characterization of the intron 1 arrest site, located 137 to 145 nucleotides downstream of the cap site. We have determined, using gel filtration, that the intron 1 arrest site is a stable RNA polymerase II pause site and that the transcription elongation factor SII promotes read-through at this site. Additionally, the sequence determinants for the pause are located within a 37-bp fragment encompassing this site (+123 to +158) and can direct transcription arrest in an orientation-dependent manner in the context of the ADA and adenovirus major late promoters. Specific point mutations in this region increase or decrease the relative pausing efficiency. We also show that the sequence determinants for transcription arrest can function when placed an additional 104 bp downstream of their natural position.
Molecular Cloning, Expression, and Functional Analysis of a cis-Prenyltransferase from Arabidopsis thaliana (2000)

cis-Prenyltransferase catalyzes the sequential condensation of isopentenyl diphosphate with allylic diphosphate to synthesize polyprenyl diphosphates that play vital roles in cellular activity. Despite potential significance of cis-prenyltransferase in plant growth and development, no gene of the enzyme has been cloned from higher plants. Using sequence information of the conserved region of cis-prenyltransferase cloned recently from Escherichia coli, Micrococcus luteus, and yeast, we have isolated and characterized the first plant cis-prenyltransferase from Arabidopsis thaliana. Sequence analysis revealed that the protein is highly homologous in several conserved regions to cis-prenyltransferases from M. luteus, E. coli, and yeast. In vitro analyses using the recombinant protein overexpressed in E. coli revealed that the enzyme catalyzed the formation of polyprenyl diphosphates ranging in carbon number from 100 to 130 with a predominance of C(120). The enzyme exhibited a higher affinity for farnesyl diphosphate than for geranylgeranyl diphosphate, with the K(m) values being 0.13 and 3.62 micrometer, respectively, but a lower affinity for isopentenyl diphosphate, with a K(m) value of 23 micrometer. In vitro rubber biosynthesis analysis indicated that the Arabidopsis cis-prenyltransferase itself could not catalyze the formation of higher molecular weight polyprenyl diphosphates similar to natural rubber. A reverse transcriptase-polymerase chain reaction analysis showed that the gene was expressed at low levels in Arabidopsis plant, in which expression of the cis-prenyltransferase in leaf and root was higher than that in stem, flower, and silique. These results indicate the tissue-specific expression of cis-prenyltransferase and suggest a potential role and significance of the enzyme in the polyisoprenoid biosynthesis in plants.
Hydrogen bonding in blends of polyesters with dipeptide‐containing polyphosphazenes (2009)

Abstract New biomedically erodible polymer composites were investigated. Polyphosphazenes containing the dipeptide side groups alanyl–glycine ethyl ester, valinyl–glycine ethyl ester, and phenylalanyl–glycine ethyl ester were blended with poly(lactide‐ co ‐glycolide) (PLGA) with lactic to glycolic acid ratios of 50 : 50 [PLGA (50 : 50)] and 85 : 15 [PLGA (85 : 15)] with solution‐phase techniques. Each dipeptide ethyl ester side group contains two NH protons that are capable of hydrogen bonding with the carbonyl functions of PLGA. Polyphosphazenes that contain only the dipeptide ethyl ester groups are insoluble in organic solvents and are thus unsuitable for solution‐phase composite formation. To ensure solubility during and after synthesis, cosubstituted polymers with both dipeptide ethyl ester and glycine or alanine ethyl ester side groups were used. Solution casting or electrospinning was used to fabricate polymer blend matrices with different ratios of polyphosphazene to polyester, and their miscibilities were estimated with differential scanning calorimetry and scanning electron microscopy techniques. Polyphosphazenes with alanyl–glycine ethyl ester side groups plus the second cosubstituent were completely miscible with PLGA (50 : 50) and PLGA (85 : 15) when processed via solution‐casting techniques. This suggests that the hydrogen‐bonding protons in alanyl–glycine ethyl ester have access to the oxygen atoms of the carbonyl units in PLGA. However, when the same pair of polymers was electrospun from solution, the polymers proved to be immiscible. Solution‐cast miscible polymer blends were obtained from PLGA (50 : 50) plus the polyphosphazene that was cosubstituted with valinyl–glycine ethyl ester and glycine ethyl ester side groups. © 2009 Wiley Periodicals, Inc. J Appl Polym Sci, 2010
Adenovirus-induced alterations of the cell growth cycle: a requirement for expression of E1A but not of E1B (1983)

Mutants dl312, dl314, hr1, and hr3 with mutations in region E1A of adenovirus type 5 were defective for the induction of cell cycle abnormalities detectable by flow cytometry, cell DNA replication, thymidine kinase production, and chromosome aberrations and did not synthesize the viral DNA-binding protein (E2A) in rat cells. dl311, a leaky E1A mutant, induced cell cycle effects at high multiplicity in only one of three experiments, and synthesized the DNA-binding protein. hr7 (E1B) gave a wild-type response in all tests. dl313 was also positive in all tests, although it induced fewer polyploid cells than did wild-type virus, probably because of the leftward extension of the dl313 E1B deletion into E1A. sub315 and sub316, with mutations which also span the E1A-E1B border, synthesized DNA-binding protein, but caused no cell cycle alterations detectable by flow cytometry in rat or mouse cells. Although the participation of other viral early regions cannot be completely excluded, our results suggest that alteration of cell cycle progression is a direct effect of E1A unrelated to its control of other viral early regions, and may be the function of E1A in transformation.
Synthesis and antibacterial activity of 1‐(2,4‐dichlorobenzoyl)‐4‐substituted thiosemicarbazides, 1,2,4‐triazoles and their methyl derivatives (1984)

Abstract A series of 1‐(2,4‐dichlorobenzoyl)thiosemicarbazides, s ‐triazoles and their methyl derivatives have been synthesised by condensation of 2,4‐dichlorobenzoyl hydrazine with aryl isothiocyanates. Subsequent ring closure of the substituted thiosemicarbazides yielded the s ‐triazoles, and reaction with methyl iodide resulted methyl derivatives. All the compounds were subjected to in vitro testing against two gram‐positive and two gram‐negative bacteria. Antibacterial activity was found to be moderate to good in most of the compounds.
Propionibacterium acnes: from Commensal to Opportunistic Biofilm-Associated Implant Pathogen (2014)

Propionibacterium acnes is known primarily as a skin commensal. However, it can present as an opportunistic pathogen via bacterial seeding to cause invasive infections such as implant-associated infections. These infections have gained more attention due to improved diagnostic procedures, such as sonication of explanted foreign materials and prolonged cultivation time of up to 14 days for periprosthetic biopsy specimens, and improved molecular methods, such as broad-range 16S rRNA gene PCR. Implant-associated infections caused by P. acnes are most often described for shoulder prosthetic joint infections as well as cerebrovascular shunt infections, fibrosis of breast implants, and infections of cardiovascular devices. P. acnes causes disease through a number of virulence factors, such as biofilm formation. P. acnes is highly susceptible to a wide range of antibiotics, including beta-lactams, quinolones, clindamycin, and rifampin, although resistance to clindamycin is increasing. Treatment requires a combination of surgery and a prolonged antibiotic treatment regimen to successfully eliminate the remaining bacteria. Most authors suggest a course of 3 to 6 months of antibiotic treatment, including 2 to 6 weeks of intravenous treatment with a beta-lactam. While recently reported data showed a good efficacy of rifampin against P. acnes biofilms, prospective, randomized, controlled studies are needed to confirm evidence for combination treatment with rifampin, as has been performed for staphylococcal implant-associated infections.
Low‐Temperature Synthesis of Highly Crystalline TiO2 Nanocrystals and their Application to Photocatalysis (2005)

Nanocrystalline TiO2 photocatalysts: We have synthesized highly crystalline TiO2 nanocrystals by the controlled sol–gel reaction of titanium tetraisopropoxide in aqueous solution at room temperature. Anatase nanorods, spherical anatase nanocrystals, and rutile nanorods were synthesized (see HRTEM image of the latter). The anatase nanorods show much better photocatalytic activities for Eosin Y, phenol photooxidation, and E. coli inactivation than Degussa P-25. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2421/2005/z400142_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Phenols and lactones in Italo-Mitcham peppermint oilMentha × piperita L. (1998)

In the acidic fractions of Italo-Mitcham black peppermint oil (Mentha × piperita L.), some uncommon phenols, carboxylic acids and lactones have been identified, mostly related to menthone. The cis/trans isomers of 2,6-dimethyl-heptan-5-olide (19 and 20) and the (6R)-5,6-dihydro-3,6-dimethyl-benzol[b]furan-7(4H)-one (27) are new compounds, their structures have been proved by syntheses; the three diastereoisomers of perhydro-3,6-dimethyl-benzo[b]furan-2-one, 16, 17 and 18 as well as 2-isopropenyl-5-methylphenol (1), have not yet been identified in a natural raw material. © 1998 John Wiley & Sons, Ltd.