gebhart/patrepeval huggingface dataset:
Analysis of clonal rearrangements of the Ig heavy chain locus in acute leukemia (1996)

Clonal rearrangements of the Ig heavy chain (IGH) locus occur in nearly all cases of B-cell precursor acute leukemia (BCP-ALL). Some of these rearrangements may be detected by polymerase chain reaction (PCR) using VH gene framework III (FRIII) and JH consensus primers. However, about 20% of BCP-ALLs fail to amplify with this technique. To determine the causes of these PCR failures and to investigate any possible association with specific subgroups of disease, we analyzed 72 acute leukemias of defined immunophenotype and cytogenetics, comparing FRIII with VH-family leader-specific PCR methods and Southern blotting. Of 37 BCP-ALL cases, 6 (16.2%) failed totally to amplify with FRIII and JH primers. None of these cases amplified with VH leader primers. Additionally, all cases retained germline VH6 genes and 5 of 11 rearranged alleles amplified with a consensus DH primer, indicating that these rearrangements represented biallelic DH-JH recombinations. Among the 6 FRIII and VH leader PCR-negative BCP-ALL cases, there was no common immunophenotype or consistent cytogenetic abnormality, although all showed structural chromosomal abnormalities and 3 of 5 successfully karyotyped had abnormalities of chromosome 12p. 13 cases with t(9;22)(q34;q11) Philadelphia chromosome-positive [Ph+]) and IGH rearrangements (9 BCP-ALL and 4 biphenotypic cases) were also analyzed. Of 23 rearranged IGH alleles, 19 (82%) were positive by FRIII PCR, and all 4 remaining alleles were amplified by VH leader primers. Use of the leader primers in these Ph+ cases also detected 3 additional clonal rearrangements that were not anticipated from Southern blotting; such unexpected bands were not observed in 21 other Ph- cases. The additional bands represented "new" and unrelated VH rearrangements rather than VH-VH replacement events. We conclude that biallelic DHJH rearrangements occur in a subgroup of BCP-ALL; in these cases, the activation of the full VHDHJH recombination mechanism had not occurred. Therefore, these cases of BCP-ALL were arrested at an early stage of B-cell differentiation. In contrast, all Ph+ BCP-ALLs and biphenotypic acute leukemias, which may represent the transformation of multipotent hemopoietic stem cells, had undergone VHDHJH recombination. Of 9 Ph+ BCP-ALL cases, 3 also showed ongoing VHDHJH rearrangement, reflecting the persistent expression of the VHDHJH recombinase. Finally, sequence analysis of 33 rearranged VHDHJH genes showed that only 3 including 2 Ph+ BCP-ALL maintained an intact open-reading frame. Loss of the open-reading frame occurred not only because of out-of-frame VHDH and DHJH joining, but also because of VH gene mutation and deletion. These data show that most BCP-ALLs may represent the neoplastic transformation of BCPs destined to die in the bone marrow.
Role of Th2 responses in the development of allergen‐induced airway remodelling in a murine model of allergic asthma (2003)

(1) To clarify the involvement of Th2 responses in the development of allergen-induced airway remodelling, we investigated the effect of anti-CD4 monoclonal antibody (mAb) and anti-CD8 mAb, and the responses of IL-4 gene-knockout (KO) mice in a murine model of allergic asthma. (2) Mice were immunized twice by intraperitoneal injections of ovalbumin (OA), and exposed to aeroallergen (OA, 1% w v(-1)) for 3 weeks. Twenty-four hours after the final challenge, airway responsiveness to acetylcholine was measured, and bronchoalveolar lavage (BAL) and histological examinations were carried out. (3) Anti-CD4 mAb (1 mg kg(-1)) clearly inhibited allergen-induced increases in airway responsiveness to acetylcholine, the number of eosinophils in BAL fluid, serum OA-specific IgE levels, IL-13 and transforming growth factor-beta1 levels in BAL fluid, and amount of hydroxyproline in the lung by 100, 99, 100, 100, 84, and 60%, respectively. Furthermore, the antibody (1 mg kg(-1)) also attenuated allergen-induced goblet cell hyperplasia in the epithelium and subepithelial fibrosis by 72 and 83%, respectively. In contrast, anti-CD8 mAb (1 mg kg(-1)) showed no effect on each parameter. Furthermore, all these parameters were attenuated in IL-4KO mice by 57, 93, 100, 45, 84 and 60%, and also 72 and 83%, respectively. (4) These findings suggest that Th2 responses play a critical role for the development of allergen-induced airway remodelling, and that the inhibition of Th2 responses, e.g. using anti-CD4 mAb, is a therapeutic approach for the treatment of airway remodelling in asthma.
Manufacturing Techniques for Microfabrication and Nanotechnology (2011)

Designed for science and engineering students, this text focuses on emerging trends in processes for fabricating MEMS and NEMS devices. The book reviews different forms of lithography, subtractive material removal processes, and additive technologies. Both top-down and bottom-up fabrication processes are exhaustively covered and the merits of the d
Differences in promiscuity for antibody–FcRn interactions across species: implications for therapeutic antibodies (2001)

Preclinical tests of therapeutic antibodies are frequently carried out in mice to evaluate pharmacokinetics and efficacy. However, the observation that mouse IgG are cleared rapidly from the human circulation suggests that mice may not always be an ideal model. The Fc receptor, FcRn, regulates the serum half-lives of IgG in mice and most likely has a similar function in humans. In the current study we have carried out an extensive analysis of the interaction of the human or mouse forms of FcRn with IgG from various species using surface plasmon resonance. We show that in contrast to mouse FcRn, human FcRn is surprisingly stringent in its binding specificity for IgG derived from different species. Human FcRn binds to human, rabbit and guinea pig IgG, but not significantly to rat, bovine, sheep or mouse IgG (with the exception of weak binding to mouse IgG2b). In contrast, mouse FcRn binds to all IgG analyzed. The lack of binding of human FcRn to mouse IgG1 has been confirmed using transfectants that have been engineered to express human FcRn on the cell surface. Our results provide a molecular explanation for the enigmatic observation that mouse IgG behave anomalously in humans. These studies have implications for the successful application of therapeutic antibodies.
Active gene sequences are undermethylated. (1981)

The degree of methylation of active regions of the chromosome has been investigated by several techniques. DNase I (deoxyribonuclease I, EC 3.1.21.1) was used to introduce nicks in the active regions of the nucleus and thereby specifically label these areas. By using the methylation-specific restriction enzymes Hpa II and Hha I it could be shown that active genes are more sensitive to these probes than are other parts of the genome. In order to measure the amount of methylation at all CpG residues, DNA was nick-translated in the presence of [alpha-32P]dGTP as the sole nucleotide source and the methylated cytosine was detected by the standard nearest-neighbor analysis. Using this assay, we found that about 70% of all CpG sequences in animal cell DNA are methylated. In active nuclear regions that are sensitive to DNase I, only 30-40% of the CpG residues are methylated. This method was also employed to study the gene sequences that are complementary to cellular RNA. By this criterion expressed gene sequences are only 20-30% methylated. These data suggest that undermethylation is a general phenomenon in all actively transcribed genes.
Overcoming Drug Resistance with Alginate Oligosaccharides Able To Potentiate the Action of Selected Antibiotics (2012)

The uncontrolled, often inappropriate use of antibiotics has resulted in the increasing prevalence of antibiotic-resistant pathogens, with major cost implications for both United States and European health care systems. We describe the utilization of a low-molecular-weight oligosaccharide nanomedicine (OligoG), based on the biopolymer alginate, which is able to perturb multidrug-resistant (MDR) bacteria by modulating biofilm formation and persistence and reducing resistance to antibiotic treatment, as evident using conventional and robotic MIC screening and microscopic analyses of biofilm structure. OligoG increased (up to 512-fold) the efficacy of conventional antibiotics against important MDR pathogens, including Pseudomonas, Acinetobacter, and Burkholderia spp., appearing to be effective with several classes of antibiotic (i.e., macrolides, β-lactams, and tetracyclines). Using confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM), increasing concentrations (2%, 6%, and 10%) of alginate oligomer were shown to have a direct effect on the quality of the biofilms produced and on the health of the cells within that biofilm. Biofilm growth was visibly weakened in the presence of 10% OligoG, as seen by decreased biomass and increased intercellular spaces, with the bacterial cells themselves becoming distorted and uneven due to apparently damaged cell membranes. This report demonstrates the feasibility of reducing the tolerance of wound biofilms to antibiotics with the use of specific alginate preparations.
Influence of solvent on the stability of silver(I)–olefin complexes (1977)

The stability constants of complexes of silver(I) with allyl alcohol, prop-2-en-1-ol, trans-but-2-en-1-ol, but-3-en-1-ol, pent-4-en-1-ol, and hex-5-en-1-ol have been determined in a number of solvents. The corresponding enthalpy and entropy changes have been evaluated. The stability constants depend on the solvent in the order propylene carbonate > water > methanol > ethanol [graphic omitted] acetonitrile, which is ascribed to competition between the unsaturated alcohol and the solvent. But-3-en-1-ol shows unexpectedly high stability constants in methanol, ethanol, and propylene carbonate which are ascribed, on the basis of entropy data, to chelate-ring formation; no chelation is obseved in water.
Rapid Assay for Microbially Reducible Ferric Iron in Aquatic Sediments (1987)

The availability of ferric iron for microbial reduction as directly determined by the activity of iron-reducing organisms was compared with its availability as determined by a newly developed chemical assay for microbially reducible iron. The chemical assay was based on the reduction of poorly crystalline ferric iron by hydroxylamine under acidic conditions. There was a strong correlation between the extent to which hydroxylamine could reduce various synthetic ferric iron forms and the susceptibility of the iron to microbial reduction in an enrichment culture of iron-reducing organisms. When sediments that contained hydroxylamine-reducible ferric iron were incubated under anaerobic conditions, ferrous iron accumulated as the concentration of hydroxylamine-reducible ferric iron declined over time. Ferrous iron production stopped as soon as the hydroxylamine-reducible ferric iron was depleted. In anaerobic incubations of reduced sediments that did not contain hydroxylamine-reducible ferric iron, there was no microbial iron reduction, even though the sediments contained high concentrations of oxalate-extractable ferric iron. A correspondence between the presence of hydroxylamine-reducible ferric iron and the extent of ferric iron reduction in anaerobic incubations was observed in sediments from an aquifer and in fresh- and brackish-water sediments from the Potomac River estuary. The assay is a significant improvement over previously described procedures for the determination of hydroxylamine-reducible ferric iron because it provides a correction for the high concentrations of solid ferrous iron which may also be extracted from sediments with acid. This is a rapid, simple technique to determine whether ferric iron is available for microbial reduction.
Comparison of different procedures for the detoxification of eucalyptus hemicellulosic hydrolysate for use in fermentative processes (2005)

Abstract Eucalyptus ( Eucalyptus grandis ) shavings were submitted to an acid hydrolysis process with the aim of obtaining a hemicellulosic hydrolysate rich in fermentable sugars. However, the hydrolysate obtained contained, in addition to sugars, several compounds that are toxic to microorganisms, namely furfural, hydroxymethylfurfural, acetic acid and phenolics. In order to produce a hydrolysate suitable for use in fermentative processes, several procedures were evaluated for hydrolysate detoxification, including concentration by vacuum evaporation and adsorption on activated charcoal, diatomaceous earths, ion‐exchange resin or adsorbent resin. Hydrolysate concentration was especially effective for furfural removal, whereas the adsorbent resin was efficient in removing hydroxymethylfurfural, phenolics and acetic acid. Combination of this resin with activated charcoal was better than with diatomaceous earths for removal of acetic acid and phenolics. The best detoxification procedure evaluated was based on hydrolysate concentration followed by adsorption on activated charcoal and adsorbent resin. By this treatment, removal rates of 82.5, 100, 100 and 94% were attained for acetic acid, furfural, hydroxymethylfurfural and phenolics, respectively. Copyright © 2005 Society of Chemical Industry
Mutational analysis of the Pseudomonas syringae pv. tomato hrpA gene encoding Hrp pilus subunit (1999)

Plant pathogenic Pseudomonas syringae strains harbour a type III secretion pathway suggested to be involved in the delivery of effector proteins from the bacteria into plant cells. During plant interaction, the bacteria apparently produce surface appendages, termed Hrp pili, that are indispensable for the secretion process. We have created an insertion mutation library, as well as deletion mutations to hrpA, the structural gene encoding Hrp pilin. Analysis of the mutants revealed gene regions important for hrpA expression, pilus assembly and pilus-dependent autoagglutination of the bacteria. The majority of insertions in the amino-terminal half of the pilin were tolerated without bacterial interaction with plants being affected, while the carboxy-terminus appeared to be needed for pilus assembly. Insertions in the 5' non-translated region and the first codons within the open reading frame affected mRNA production or stability and abolished protein production.
Fatty Acid Composition of Lipids in Sea Buckthorn (Hippophaë rhamnoides L.) Berries of Different Origins (2001)

The oil content and fatty acid composition of berries from two subspecies of sea buckthorn (Hippophaë rhamnoides L.) were investigated. The berries of subsp. rhamnoides contained a higher proportion of oil in seeds (11.3% vs 7.3%, p < 0.01), berries (3.5% vs 2.1%, p < 0.001), and seedless parts (2.8% vs 1.7%, p < 0.01) than the berries of subsp. sinensis. Linoleic (18:2n-6) and alpha-linolenic acids (18:3n-3) comprised about 70% of seed oil fatty acids. Palmitoleic acid (16:1n-7), practically absent in the seed oil, comprised 12.1--39.0% of oil in pulp/peel and 8.9--31.0% of that in the whole berries. More linoleic acid (40.9% vs 39.1%) and less alpha-linolenic acid (26.6% vs 30.6%) was found in the seed oil of subsp. sinensis than in the seed oil of subsp. rhamnoides (p < 0.05). The proportion of palmitoleic acid was higher in the oil of berries of subsp. rhamnoides than the berries of subsp. sinensis (26.0% vs 21.5%, 0.05 < p < 0.1), but was vice versa with alpha-linolenic acid (8.8% vs 11.2%, 0.05 < p < 0.1). The proportions of alpha-linolenic acid correlated inversely with oleic and linoleic acids in the seed oil. In the oil of whole berries, the proportion of palmitoleic acid correlated negatively with the proportions of linoleic and alpha-linolenic acids.
Detection and Identification of Breast Cancer Volatile Organic Compounds Biomarkers Using Highly-Sensitive Single Nanowire Array on a Chip (2013)

A single nanowire array on a chip with different materials of Palladium, Polypyrrole and Zinc Oxide has been fabricated using electrochemical deposition method. The fabricated single nanowire array has been demonstrated for highly sensitive and specific diagnosis of breast cancer by detecting four volatile organic compound biomarkers: Heptanal, Acetophenone, Isopropyl Myristate and 2-Propanol. The demonstrated sensing limits for Heptanal, Acetophenone, Isopropyl Myristate and 2-propanol using individual Palladium, Polypyrrole and Zinc Oxide nanowires were 8.982 ppm, 798 ppb, 134 ppm, and 129.5 ppm, respectively, and the corresponding sensitivities of resistance change were in the range of 0.3%-5% which indicated excellent sensing performance of the single nanowires. The response time for Palladium, Polypyrrole and Zinc Oxide nanowires to achieve maximum conductance change was less than 200 seconds while also illustrating excellent signal repeatability. With the principal component analysis of the resistance change versus time in each detection period of the nanowire array, the smell prints for the four volatile organic compounds biomarkers of Breast Cancer are discriminated in the 3-D plots.
A New Atropisomeric P,N Ligand for Rhodium-Catalyzed Asymmetric Hydroboration (2002)

A new optically active and large dihedral angle atropisomeric P,N ligand, pyphos, which contains a tertiary phosphine and pyridine moiety, was prepared and resolved through diastereomeric complexation with chiral palladium amine complexes. The hexafluorophosphate salt of the diastereomers were found to be separable by fractional recyrstallization, while the corresponding chloride salt did not. [Rh(COD)pyphos]PF(6) complex was synthesized by metalation of pyphos with [Rh(COD)Cl](2) followed by anion exchange with NH(4)PF(6) in excellent yield, and the target rhodium complex was characterized by single-crystal X-ray crystallography. The chiral cationic rhodium complex was utilized in the enantioselective hydroboration of vinylarenes. Excellent regioselectivity and good enantioselectivity were observed, and the ee values were found to be dependent on the electronic properties of para-substituted styrenes.
Adaptive overload control for busy internet servers (2003)

As Internet services become more popular and pervasive, a critical problem that arises is managing the performance of services under extreme overload. This paper presents a set of techniques for managing overload in complex, dynamic Internet services. These techniques are based on an adaptive admission control mechanism that attempts to bound the 90th-percentile response time of requests flowing through the service. This is accomplished by internally monitoring the performance of the service, which is decomposed into a set of event-driven stages connected with request queues. By controlling the rate at which each stage admits requests, the service can perform focused overload management, for example, by filtering only those requests that lead to resource bottlenecks. We present two extensions of this basic controller that provide class-based service differentiation as well as application-specific service degradation. We evaluate these mechanisms using a complex Webbased e-mail service that is subjected to a realistic user load, as well as a simpler Web server benchmark.
A new antiestrogen, 2-(4-hydroxy-phenyl)-3-methyl-1-[4-(2-piperidin-1-yl-ethoxy)-benzyl]-1H-indol-5-ol hydrochloride (ERA-923), inhibits the growth of tamoxifen-sensitive and -resistant tumors and is devoid of uterotropic effects in mice and rats. (2001)

In preclinical models, ERA-923 has an improved efficacy and safety compared with tamoxifen. Clinical trials with ERA-923 are in progress.
Spanning the gap between motion estimation and morphing (2002)

Motion estimation is an important and well-studied method for determining correspondences between images in video processing. In contrast with motion estimation, the use of image warping on image sequences is a new and developing field. To provide image warping effects, morphing algorithms rely on mesh points to align two images. Presently, the selection of these mesh points is a labor-intensive, manual process. This paper attempts to automate the selection of mesh points for morphing by recognizing this problem as one of determining image correspondences. Applications include video compression, animation sequence generation and high-quality time dilation of video.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Electropolymerized 1,2-diaminobenzene as a means to prevent interferences and fouling and to stabilize immobilized enzyme in electrochemical biosensors (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTElectropolymerized 1,2-diaminobenzene as a means to prevent interferences and fouling and to stabilize immobilized enzyme in electrochemical biosensorsSylvia V. Sasso, Raymond J. Pierce, Robert. Walla, and Alexander M. YacynychCite this: Anal. Chem. 1990, 62, 11, 1111–1117Publication Date (Print):June 1, 1990Publication History Published online1 May 2002Published inissue 1 June 1990https://pubs.acs.org/doi/10.1021/ac00210a004https://doi.org/10.1021/ac00210a004research-articleACS PublicationsRequest reuse permissionsArticle Views1117Altmetric-Citations283LEARN 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
Evidence for Dinucleotide Flipping by DNA Photolyase (1998)

DNA photolyases repair pyrimidine dimers via a reaction in which light energy drives electron donation from a catalytic chromophore, FADH-, to the dimer. The crystal structure of Escherichia coli photolyase suggested that the pyrimidine dimer is flipped out of the DNA helix and into a cavity that leads from the surface of the enzyme to FADH-. We have tested this model using the Saccharomyces cerevisiae Phr1 photolyase which is >50% identical to E. coli photolyase over the region comprising the DNA binding domain. By using the bacterial photolyase as a starting point, we modeled the region encompassing amino acids 383-530 of the yeast enzyme. The model retained the cavity leading to FADH- as well as the band of positive electrostatic potential which defines the DNA binding surface. We found that alanine substitution mutations at sites within the cavity reduced both substrate binding and discrimination, providing direct support for the dinucleotide flip model. The roles of three residues predicted to interact with DNA flanking the dimer were also tested. Arg452 was found to be particularly critical to substrate binding, discrimination, and photolysis, suggesting a role in establishing or maintaining the dimer in the flipped state. A structural model for photolyase-dimer interaction is presented.