gebhart/patrepeval huggingface dataset:
Metabolism of 4-chloro-2-methylphenoxyacetate by a soil pseudomonad. Preliminary evidence for the metabolic pathway (1971)

1. A pseudomonad capable of utilizing the herbicide 4-chloro-2-methylphenoxyacetate as a sole carbon source was isolated from soil and cultured in liquid medium. 2. Analysis of induction patterns of 4-chloro-2-methylphenoxyacetate-grown cells suggests that 5-chloro-o-cresol and 5-chloro-3-methylcatechol are early intermediates in the oxidation of 4-chloro-2-methylphenoxyacetate. Cells were not adapted to oxidize 4-chloro-6-hydroxy-2-methylphenoxyacetate. 3. In culture, 4-chloro-2-methylphenoxyacetate rapidly disappeared and the chlorine in the molecule was quantitatively released as Cl(-) ion. 4. A lactone (gamma-carboxymethylene-alpha-methyl-Delta(alphabeta)-butenolide) was isolated from cultures and established as an intermediate. 5. The following metabolic pathway is suggested: 4-chloro-2-methylphenoxyacetate --> 5-chloro-o-cresol --> 5-chloro-3-methylcatechol --> cis-cis-gamma-chloro-alpha-methylmuconate --> gamma-carboxymethylene-alpha-methyl-Delta(alphabeta)-butenolide --> gamma-hydroxy-alpha-methylmuconate. 6. The tentative identification of 5-chloro-o-cresol, a gamma-chloro-alpha-methylmuconate and gamma-hydroxy-alpha-methylmuconate in culture extracts supports this scheme. However, the catechol was never observed to accumulate in cultures. 7. The detection of 4-chloro-6-hydroxy-2-methylphenoxyacetate, 2-methyl-phenoxyacetate, a dehalogenated cresol and oxalate in culture extracts is discussed in relation to the proposed metabolic pathway.
Fusion Peptides Derived from the HIV Type 1 Glycoprotein 41 Associate within Phospholipid Membranes and Inhibit Cell-Cell Fusion (1997)

The fusion domain of human immunodeficiency virus (HIV-1) envelope glycoprotein (gp120-gp41) is a conserved hydrophobic region located at the N terminus of the transmembrane glycoprotein (gp41). A V2E mutant has been shown to dominantly interfere with wild-type envelope-mediated syncytium formation and virus infectivity. To understand this phenomenon, a 33-residue peptide (wild type, WT) identical to the N-terminal segment of gp41 and its V2E mutant were synthesized, fluorescently labeled, and characterized. Both peptides inhibited HIV-1 envelope-mediated cell-cell fusion and had similar alpha-helical content in membrane mimetic environments. Studies with fluorescently labeled peptide analogues revealed that both peptides have high affinity for phospholipid membranes, are susceptible to digestion by proteinase-K in their membrane-bound state, and tend to self- and coassemble in the membranes. In SDS-polyacrylamide gel electrophoresis the WT peptide formed dimers as well as higher order oligomers, whereas the V2E mutant only formed dimers. The WT, but not the V2E mutant, induced liposome aggregation, destabilization, and fusion. Moreover, the V2E mutant inhibited vesicle fusion induced by the WT peptide, probably by forming inactive heteroaggregates. These data form the basis for an explanation of the mechanism by which the gp41 V2E mutant inhibits HIV-1 infectivity in cells when co-expressed with WT gp41.
Use of an on-column frit in capillary zone electrophoresis: sample collection (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTUse of an on-column frit in capillary zone electrophoresis: sample collectionXiaohua. Huang and Richard N. ZareCite this: Anal. Chem. 1990, 62, 5, 443–446Publication Date (Print):March 1, 1990Publication History Published online1 May 2002Published inissue 1 March 1990https://pubs.acs.org/doi/10.1021/ac00204a005https://doi.org/10.1021/ac00204a005research-articleACS PublicationsRequest reuse permissionsArticle Views117Altmetric-Citations73LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Orientational Transition of Liquid Crystal Molecules by a Photoinduced Transformation Process into a Recovery‐free Silicon Oxide Layer (2008)

The vertical alignment of liquid crystal (LC) on an inorganic silicon oxide layer, which is fabricated by a simple photoinduced transformation process of an ultrathin poly(dimethylsiloxane) (PDMS) layer is reported. While the PDMS layer shows a random orientation of LC, the silicon oxide layer, fabricated by UVO treatment, vertically aligns the LC. In addition, the silicon oxide layer shows a stable alignment of LC in harsh conditions. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2089/2008/adma200702906_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.
A B Cell-Based Sensor for Rapid Identification of Pathogens (2003)

We report the use of genetically engineered cells in a pathogen identification sensor. This sensor uses B lymphocytes that have been engineered to emit light within seconds of exposure to specific bacteria and viruses. We demonstrated rapid screening of relevant samples and identification of a variety of pathogens at very low levels. Because of its speed, sensitivity, and specificity, this pathogen identification technology could prove useful for medical diagnostics, biowarfare defense, food- and water-quality monitoring, and other applications.
Mixed Carboxylic Acid Production by Megasphaera elsdenii from Glucose and Lignocellulosic Hydrolysate (2017)

Volatile fatty acids (VFAs) can be readily produced from many anaerobic microbes and subsequently utilized as precursors to renewable biofuels and biochemicals. Megasphaera elsdenii represents a promising host for production of VFAs, butyric acid (BA) and hexanoic acid (HA). However, due to the toxicity of these acids, product removal via an extractive fermentation system is required to achieve high titers and productivities. Here, we examine multiple aspects of extractive separations to produce BA and HA from glucose and lignocellulosic hydrolysate with M. elsdenii. A mixture of oleyl alcohol and 10% (v/v) trioctylamine was selected as an extraction solvent due to its insignificant inhibitory effect on the bacteria. Batch extractive fermentations were conducted in the pH range of 5.0 to 6.5 to select the best cell growth rate and extraction efficiency combination. Subsequently, fed-batch pertractive fermentations were run over 230 h, demonstrating high BA and HA concentrations in the extracted fraction (57.2 g/L from ~190 g/L glucose) and productivity (0.26 g/L/h). To our knowledge, these are the highest combined acid titers and productivity values reported for M. elsdenii and bacterial mono-cultures from sugars. Lastly, the production of BA and HA (up to 17 g/L) from lignocellulosic sugars was demonstrated.
Carbohydrates of lysosomal enzymes secreted by Tetrahymena pyriformis. (1985)

The carbohydrate structures of acid phosphatase and alpha-glucosidase secreted into culture medium by Tetrahymena pyriformis strain W were studied. Their asparagine-linked sugar chains were quantitatively liberated as radioactive oligosaccharides from their polypeptide moieties by controlled hydrazinolysis followed by N-acetylation and NaB3H4 reduction. The approximate amounts of total sugar chains liberated from 1 mol each of acid phosphatase and alpha-glucosidase were 6 and 4 mol, respectively. Paper electrophoresis revealed that only neutral oligosaccharides were obtained from both enzymes. The oligosaccharide fraction from acid phosphatase was separated into seven components by Bio-Gel P-4 column chromatography while that from alpha-glucosidase was resolved into three components. The structures of these oligosaccharides were determined by sequential glycosidase digestion in combination with methylation analysis. The sugar chains of the two enzymes can be primarily classified as high mannose-type oligosaccharides. However, they have the following characteristic features: 1) their common core is not the usual Man5 . GlcNAc2 structure, it is Man3 . GlcNAc2; 2) some of the sugar chains of acid phosphatase have 1 approximately 3 glucose residues linked to the nonreducing terminal Man alpha 1----2 residue. The structural characteristics of the sugar moieties of the two enzymes indicate that they might be produced by the so-called "alternate pathway," in which lipid-linked Glc3 . Man5 . GlcNAc2 functions as an oligosaccharide donor.
Adeno-Associated Virus Serotype 6 Capsid Tyrosine-to-Phenylalanine Mutations Improve Gene Transfer to Skeletal Muscle (2010)

Adeno-associated viral (AAV) vectors are the most efficient in vivo gene transfer tools for gene therapy applications. Efforts have been made to translate encouraging results in small animal models to human patients. However, the need for large quantities of vector for clinical application remains a great challenge. Developing novel AAV vectors with enhanced infectivity may reduce the high vector dose requirement for many applications such as gene therapy for muscular dystrophy. Selective mutation of AAV capsid surface-exposed tyrosine (Y) is a novel strategy to improve transduction efficiency. AAV6 has been considered one of the most robust muscle gene delivery vehicles. Here, we hypothesize that AAV6 transduction efficiency can be further enhanced by mutating surface Y to phenylalanine (F). We found that mutants AAV6-Y445F and AAV6-Y731F, especially the former, achieved more efficient gene transfer than the original AAV6 after intramuscular administration to mice. Expression of both firefly luciferase and alkaline phosphatase reporter genes increased up to 8-fold and DNA copy numbers in muscle increased up to 6-fold. Our results suggest that tyrosine-mutant AAV6 vectors may represent powerful tools for testing muscle gene therapy in animal models and potentially in humans.
The application of transform methods to Hippuran renograms (1978)

Transform methods have recently been applied to Hippuran renograms assuming a two-component exponential plasma clearance curve (Fleming and Goddard 1974) and a three-component curve (van Stekelenburg 1978). The author points out that the form of the activity equations is independent of the model chosen.
On the SelectiveN-Methylation of BOC-Protected Amino Acids (2009)

The selective N-methylation of BOC-protected valine 1a with MeI and NaH in THF (i.e., in the presence of a free carboxyl group) has been attributed to the protection of the carboxylate by chelation to Na(+). An alternative mechanism, involving the formation of the carbene intermediate generated from MeI and its insertion into the N-H bond, has been ruled out by isotopic labeling.
Allelic and locus heterogeneity in inherited venous malformations (1999)

Venous malformations are low-flow vascular lesions consisting of disorganized thin-walled vascular channels. These can occur sporadically but also as an autosomal dominant condition termed venous malformations, cutaneous and mucosal (VMCM; OMIM 600195). In two large unrelated kindreds mapping to chromosome 9, the identical R849W missense mutation was identified in the first kinase domain of Tie2, an endothelial cell-specific receptor tyrosine kinase. We report here the identification of four new kindreds with inherited venous malformations. Unlike the initial two families described, these four families demonstrate allelic and locus heterogeneity. In one of these families, the R849W mutation co-segregates with the disease phenotype. Three other families with venous malformations lack this mutation. One of these families is linked to markers near TIE2 on chromosome 9. In this family, we identified a novel mutation within the first kinase domain of Tie2 resulting in a Y897S change. Results from COS-1 cell transfections using expression constructs containing either the R849W or the Y897S mutation suggest that the receptors containing either mutation show ligand-independent hyperphosphorylation. These results suggest a gain-of-function mechanism for development of venous malformations in these families. Of the two remaining families, one excludes linkage to the TIE2 locus, establishing the existence of at least one additional locus for dominantly inherited venous malformations.
Cerebrovascular projections from the sphenopalatine and otic ganglia to the middle cerebral artery of the cat. (1986)

The location of the postganglionic parasympathetic cell bodies projecting to cerebral arteries is unknown. Using axonal tracing techniques, we examined whether the sphenopalatine ganglia (associated with the seventh cranial nerve) and otic ganglia (associated with ninth cranial nerve) contain perikarya which send axons to the feline middle cerebral artery (MCA). The tracers horseradish peroxidase (HRP: 3 cats) or wheat germ agglutinin (WGA: 6 cats) were applied to the MCA in a slow release polymeric system. Three days later the SPG, otic ganglia, and rete mirabile were harvested bilaterally and processed for tracer by the TMB method (HRP) or immunohistochemistry (WGA). In a given animal, approximately equal numbers of cells containing axonal tracer were found in both SPG. Labeled fibers occasionally could be seen extending into the vidian nerve. Positive cells were also found in the otic ganglia and in the walls of the internal rete mirabile. These results provide the first identification of parasympathetic cell bodies projecting to cerebral blood vessels.
¿Comprenden los estudiantes las gráficas cartesianas usadas en los textos de ciencias? (2008)

Este artículo presenta los resultados de una investigación acerca del desempeño de los estudiantes de bachillerato y de licenciatura en química, en nueve tareas de interpretación de gráficas cartesianas incluidas en los libros de texto de química usados en el bachillerato. El estudio muestra que los participantes en el estudio no tienen dificultad para llevar a cabo las tareas de identificación de variables, lectura de datos y clasificación de la relación entre las variables. Sin embargo, los participantes presentan dificultad en tareas como la identificación de la relación entre las variables, el reconocimiento de los términos incluidos en la gráfica o la elaboración de conclusiones, explicaciones y predicciones a partir de la información gráfica. Así mismo, el estudio muestra que el aumento de complejidad de las tareas y algunas características de las gráficas (v.g. las líneas curvas o su uso instrumental en trabajos prácticos) hacen más difícil la ejecución de las tareas para los participantes en el estudio.
A Tetraspan Membrane Glycoprotein Produced in the Human Intestinal Epithelium and Liver That Can Regulate Cell Density-dependent Proliferation (1995)

The human cell line HT-29 provides a model system for studying regulation of proliferation and differentiation in intestinal epithelial cell lineages: (i) HT-29 cells cultured in glucose resemble undifferentiated multipotent transit cells located in the lower half of intestinal crypts; (ii) proliferating HT-29 cells cultured in inosine resemble committed cells located in the upper half of the crypt; (iii) nonproliferating, confluent HT-29-inosine cells have features of differentiated enterocytes and goblet cells that overlie small intestinal villi. A cDNA library prepared from HT-29-inosine cells was screened with a series of subtracted cDNA probes to identify proteins that regulate proliferation/differentiation along the crypt-villus axis. A cDNA was recovered that encodes a 202-amino acid protein with four predicted membrane spanning domains and two potential sites for N-linked glycosylation. Levels of this new member of the superfamily of tetraspan membrane proteins (TMPs) increase dramatically as nondividing epithelial cells exit the proliferative compartment of the crypt-villus unit and migrate onto the villus. The protein is also produced in nondividing hepatocytes that have the greatest proliferative potential within liver acini. Three sets of observations indicate that in the appropriate cellular context, intestinal and liver (il)-TMP can mediate density-associated inhibition of proliferation. (i) Accumulation of il-TMP glycoforms precedes terminal differentiation of HT-29-inosine cells and occurs as they undergo density-dependent cessation of growth. il-TMP levels are lower and glycosylation less extensive in HT-29-glucose cells, which do not undergo growth arrest at confluence. (ii) HeLa cells normally do not produce il-TMP. Forced expression of il-TMP inhibits proliferation as cells approach confluence. The extent of il-TMP glycosylation in the transfected cells is similar to that observed in HT-29-inosine cells and greater than in HT-29-glucose cells. (iii) SW480 cells are derived from a human colon adenocarcinoma and do not express il-TMP. Like nontransfected HeLa cells, they do not stop dividing at confluence, whether grown in medium containing glucose or inosine. Expression of il-TMP has no effect on the growth properties of SW480 cells. The extent of il-TMP glycosylation in SW480-glucose cells is similar to that noted in HT-29-glucose cells, lending further support to the notion that il-TMP's activity is related to its state of N-glycosylation.
Intracellular disruption of mitochondria in a living HeLa cell with a 76-MHz femtosecond laser oscillator (2005)

Femtosecond laser pulses can be used to selectively disrupt and dissect intracellular organelles. We report on disruption of mitochondria in living HeLa cells using a femtosecond laser oscillator with a repetition rate of 76 MHz. We studied the laser parameters used for disruption. The longterm viability of the cells after disruption of a single mitochondrion was confirmed by the observation of cell division, indicating that intracellular disruption of organelles using a femtosecond laser oscillator can be performed without compromising the long-term cell viability.
Detection and elimination of cellular nucleic acids in biologicals produced on continuous cell lines. (1981)

Experiments have been conducted to determine the extent to which currently available purification techniques can remove contaminating substrate cellular DNA from inactivated poliovirus vaccine produced on continuous cell lines rising highly [32P]-labeled, nick-translated cellular DNA added to poliovirus suspensions, we found that purification procedures were capable, in small-scale experiments, of reducing contaminating DNA by factors of 10(3) (DNAse treatment followed by gel filtration) and 10(3)-3X10(5) (ion exchange chromatography). Sequential application of these purification steps should reduce contaminating cellular DNA to acceptable levels. We also examined the potential usefulness of immobilized nucleic acid hybridization techniques for the routine direct testing of residual cellular nucleic acids in final production lots of inactivated poliovirus vaccine and other biologicals. A filter hybridization test, using [32P]-labeled, nick-translated cellular DNA as a probe, was capable of detecting 40 pg of homologous cellular DNA. Using probes of higher specific activity the assay should be sensitive enough for use in routine quality control.
A Versatile and Scalable Two-Step Ion-Exchange Chromatography Process for the Purification of Recombinant Adeno-associated Virus Serotypes-2 and -5 (2002)

Here we describe the development of a two-step chromatography process based on the use of ion-exchange resins for the purification of recombinant adeno-associated virus (rAAV) serotypes-2 and -5. In vitro and in vivo results demonstrate that this method, which does not require any prepurification step of the cell lysate, can be applied to obtain highly pure rAAV2 and rAAV5 stocks. As such, this procedure can be easily transferred in vector cores and also scaled up, allowing the direct comparison of these two, and potentially other, AAV serotypes in large animal models.
Human genetic disease analysis: a practical approach (1993)

Part 1 Foetal DNA analysis, J.M. Old: chorionic villi DNA - sampling and shipment, DNA preparation, DNA yield amniocyte DNA - choice of sample, DNA preparation other DNA sources quick DNA preparation for PCR storage of DNA DNA analysis - southern blot analysis, polymerase chain reaction potential problems - maternal DNA contamination, plasmid and target DNA contamination, technical difficulties, non-paternity. Part 2 The use of synthetic oligonucleotides as specific hybridization probes the diagnosis of genetic disorders, S.W. Thein, et al: principle of oligonucleotide hybridization oligonucleotide probe design detection of target DNA sequence - preparation of oligonucleotide probe, oligonucleotide probe hybridization, an alternative hybridization - competition hybridization practical applications - polymorphism the c-erb-B2 transmembrane region, specificity of competition hybridization. Part 3 Pulsed-field gel electrophoresis the analysis of genomic DNA and YAC clones, J.T. den Dunnen et al: available PFGE systems preparation of DNA samples - isolation of DNA agarose, preparation of marker DNAs, restriction digestion of agarose-embedded DNA electrophoresis - the PFGE system, gel preparation, planned DNA separations, blotting of PFGE gels, hybridization of PFGE gels, rehybridization of PFGE blots PFGE applications - analysis of chromosomal (human) DNA, YAC technology, further applications future developments. Part 4 Fluorescent in situ hybridization, V.J. Buckle and K.A. Rack: practical considerations - chromosome and nuclei preparation, pre-hybridization procedures, DNA resources for use as probes, probe labelling, hybridization, signal detection, chromosome banding, visualization of signal, analysis of signal, trouble-shooting applications - direct localization within the genome, sequence order on the chromosome, structural chromosome abnormalities, numerical chromosome abnormalities, chromosome painting, nuclear organization, other applications. Part 5 Fine mapping of genes - the characterization of the transcriptional unit, M. Antoniou, et al: cDNA and genomic DNA clones mapping the transcriptional unit - restriction map, northern blots, run-on transcription, R looping, nuclease Sl protection and southern blots, nuclease Sl protection of end-labelled probes, exonuclease VII, T7, T3 or SP6 polymerase probes, primer extensions polymerase chain reaction (PCR). Part 6 Chromosome analysis and sorting by flow cytometry, S. Monard et al: instrumentation - safety discussion.