gebhart/patrepeval huggingface dataset:
Determination of Three-Dimensional Structures of Proteins and Nucleic Acids in Solution by Nuclear Magnetic Resonance Spectroscop (1989)

Nuclear magnetic resonance (NMR) spectroscopy has evolved over the last decade into a powerful method for determining three-dimensional structures of biological macromolecules in solution. Key advances have been the introduction of two-dimensional experiments, high-field superconducting magnets, and computational procedures for converting the NMR-derived interproton distances and torsion angles into three-dimensional structures. This article outlines the methodology employed, describes the major NMR experiments necessary for the spectral analysis of macromolecules, and discusses the computational approaches employed to date. The present state of the art is illustrated using a variety of examples, and future developments are indicated.
Naturally Occurring Scaffolds for Soft Tissue Repair and Regeneration (2002)

Cell growth supports (i.e., scaffolds) that provide a conducive environment for normal cellular growth, differentiation, and angiogenesis are important components of tissue engineered grafts because rapid integration with the host is essential for long-term graft viability. While many of these scaffold materials are synthetic biodegradable polymers, others are naturally derived from mammalian tissue sources. Naturally occurring scaffold materials include small intestinal submucosa, acellular dermis, amniotic membrane tissue, cadaveric fascia, and the bladder acellular matrix graft. Upon implantation, these materials elicit a host-tissue response that initiates angiogenesis, encourages tissue deposition and culminates in restoration of structure and function specific to the grafted site. The sources, the methods of procurement and processing, and the effects of these naturally occurring materials on angiogenesis and tissue deposition are reviewed.
An Adaptive Testing Simulation for a Certifying Examination. (1992)

This study examined performance of a simulated computerized adaptive test that was designed to help direct the development of a medical recertification examination. The item pool consisted of 229 single-best-answer items from a random sample of 3,000 examinees, calibrated using the two-parameter logistic model. Examinees' responses were known. For tests of 60, 120, and 180 items, estimation error and the accuracy of pass/fail classification decisions were studied. Ability estimates were stable across test length changes, and accurate estimates were obtained with all three test lengths. However, it is recommended that overall pass/fail decisions be based on longer tests, especially when the cutscore is close to the mean. This initial application suggests that computerized adaptive testing has promise in professional evaluation settings. Six tables present study data, and there is a 10-item list of references. (Author/SIM) *111***************************R***********M!************************** Reproductions supplied by EDRS are the best that can be made from the original document. *******************************************WASM**********************
Control of grapevine powdery mildew with mineral oil: an assessment of oil concentration and spray volume (1999)

DC Tron, a highly refined mineral oil containing patented additives to prevent UV light induced breakdown, was evaluated in vineyards for control of powdery mildew. DC Tron suppressed development of powdery mildew but was not as effective as the conventional fungicide Topas. Of the oil treatments the 1% rate applied in spray volumes of 1000 L/ha was the most efficient. Poor control was achieved with oil rates less than 1% as well as spray volumes less than 1000 L/ha whereas phytotoxicity developed in many cases at concentrations greater than 1% or spray volumes higher than 1000 L/ha. In all oil treatments, powdery mildew developed less in leaves than on bunches. This difference was attributed to poor spray coverage on bunches compared to leaves.
High-throughput profiling of influenza A virus hemagglutinin gene at single-nucleotide resolution (2014)

Genetic research on influenza virus biology has been informed in large part by nucleotide variants present in seasonal or pandemic samples, or individual mutants generated in the laboratory, leaving a substantial part of the genome uncharacterized. Here, we have developed a single-nucleotide resolution genetic approach to interrogate the fitness effect of point mutations in 98% of the amino acid positions in the influenza A virus hemagglutinin (HA) gene. Our HA fitness map provides a reference to identify indispensable regions to aid in drug and vaccine design as targeting these regions will increase the genetic barrier for the emergence of escape mutations. This study offers a new platform for studying genome dynamics, structure-function relationships, virus-host interactions, and can further rational drug and vaccine design. Our approach can also be applied to any virus that can be genetically manipulated.
Lewis-base silane activation: from reductive cleavage of aryl ethers to selective ortho-silylation (2013)

We report a transition-metal-free protocol for the efficient reductive cleavage of diaryl and aryl alkyl ethers. The combination of triethylsilane with common bases forms an unusually powerful reductive couple that regioselectively ruptures lignin- and coal-related C–O bonds in aromatic ethers. Interestingly, with certain bases and temperature regimes ortho-directed C–H silylation efficiently competes with the latter process. However, careful tuning of the reactions conditions allows for the selective reductive cleavage of lignin model compounds to their corresponding phenolic and aromatic constituents.
Most multifocal papillary thyroid carcinomas acquire genetic and morphotype diversity through subclonal evolution following the intra‐glandular spread of the initial neoplastic clone (2008)

Papillary thyroid carcinoma (PTC) is frequently multifocal (mPTC), with synchronous tumour foci often showing varied morphology. The genetic mechanisms underlying the development of multiple and histologically diverse tumour foci remain uncertain. Different tumour foci might develop either through intrathyroidal dissemination of a single malignant clone, with morphotype differentiation occurring as a result of subclonal progression, or they may stem from independent transformational events involving multiple progenitor clones. To determine the clonal derivation of multiple tumour foci and to map their clonal relationships and genetic progression in mPTC, we evaluated genome-wide allelic imbalances (AI) and BRAF V600E mutation status in 55 synchronous tumour foci from 18 mPTC patients. For apparently monoclonal tumours, we calculated the probabilities of monoclonal derivation and used phylogenetic analysis to model clonal evolution. Genome-wide allelotyping and BRAF mutation analysis showed genetic alterations consistent with monoclonal origin in 83% of cases, mostly with evidence of subclonal evolution. BRAF V600E mutations were early events during clonal evolution of most, but not all cases. MPTC with morphologically diverse tumour foci also arose through monoclonal derivation in 75% of cases, demonstrating that morphotype-determining genetic changes can be acquired during clonal diversification, subsequent to the spread of the original malignant progenitor clone. In 17% of patients, discordant AI or BRAF V600E profiles implied that mPTCs can occasionally develop from distinct transformation events. This study suggests that mPTC originates usually from neoplastic transformation and subsequent intrathyroidal spread of a single malignant progenitor clone. Clonal progression and morphotype differentiation occur through progressive acquisition of genetic alterations subsequent to the initial intra-glandular spread. In monoclonal BRAF V600E-positive mPTCs, BRAF V600E is not always present in all tumour foci, indicating that other tumour-genetic factors in the primary progenitor clone can also trigger PTC neoplastic transformation.
A serine/threonine kinase activity is closely associated with a 65-kDa phosphoprotein specifically recognized by the kappa B enhancer element (1991)

The immunoglobulin kappa light chain enhancer, kappa B, is an important cis-acting transcriptional element. kappa B binds a number of proteins including the members of the ubiquitous NF-kappa B family of transcription factors. Agarose beads coupled to a double-stranded oligonucleotide containing the kappa B motif were used to isolate a 65-kDa predominantly nuclear phosphoprotein. Southwestern blot analysis demonstrated that this phosphoprotein can bind the kappa B element directly and specifically. This kappa B-associated protein was phosphorylated in vivo and in vitro by a nuclear serine/threonine kinase(s) which, in a number of different cell lines, appeared to be stimulated in response to interleukin-1 alpha and lipopolysaccharide treatment. In the B cell lines 70Z/3 and CH12 LX2B, and the T cell line EL-4 6.1 C10 the activity of the kappa B-associated kinase(s) correlated with the binding activity of nuclear NF-kappa B displayed in a gel shift assay. In vitro, the 65-kDa protein was phosphorylated in the absence of exogenously added kinase. The 65-kDa phosphoprotein and the kinase activity remained associated following sequential anion-exchange and hydrophobic interaction chromatography. These results suggest that the kappa B-associated phosphoprotein is either autophosphorylated or is phosphorylated by a closely associated kinase(s). Stimulation of a nuclear protein kinase which is closely associated with a sequence-specific DNA may reflect a novel mechanism by which growth factors regulate gene expression.
Clonally related IgE and IgG4 transcripts in blood lymphocytes of patients with asthma reveal differing patterns of somatic mutation (1998)

Isotype switching to IgE contributes to atopic asthma, therefore strategies to divert this process to alternative isotypes could have therapeutic relevance. It is known that patients with allergic disease have serum IgE and IgG4 antibodies with similar specificities, and that cytokines such as IL-4 mediate switching to both of these isotypes. Availability of variable region gene analysis has allowed us to probe isotype variants at the single-cell level. An earlier report described identification in a single atopic patient of short transcripts with a common complementarity-determining region "clonal signature" in combination with C mu, C gamma4 and C epsilon. We have extended this analysis, and have identified V(H)-Cgamma4 transcripts with clear clonal relationship to IgE-derived sequences in blood lymphocytes from three of four patients with atopic asthma. No other IgG subclasses were detected, confirming the link between IgE and IgG4. Full sequences were obtained from each clonally related isotype in all patients, and showed extensive somatic mutation. As previously found for IgE, the IgG4 isotypes had evident intraclonal variation. There were shared mutations between isotypes, but also many differences, indicative of separate cell populations with divergent mutational histories. These findings indicate that, in atopic patients, an individual B cell commonly switches to either IgE or IgG4. Cells producing each isotype then co-exist in the recirculating pool, and the balance between them may influence the disease process.
Improved Technique for Detection of Enhanced Green Fluorescent Protein in Transgenic Mice (2001)

One of the most exciting recent advances in cell biology is the possibility to use the green fluorescent protein and its various mutated forms as reporter proteins in studies carried out in vitro and in vivo. In the present study, several detection techniques for the enhanced green fluorescent protein (EGFP) were compared in transgenic mice, using fluorescence and confocal microscopy. In addition, different tissue preparation techniques (squash preparations, vibratome sections, frozen sections) were evaluated. As a model we used transgenic mice expressing EGFP under the control of a 5.0-kb fragment of the glutathione peroxidase isoenzyme 5 protein promoter (GPX5-EGFP) or under a 3.8-kb fragment of the cysteine rich protein-1 promoter (CRISP1-EGFP). In the GPX5-EGFP mice, expression of EGFP was observed in the distal part of the caput epididymis, while the CRISP1 promoter directed EGFP expression in the tubular compartment of the testis. Among the various tissue preparation procedures tested, the best morphological and histological preservation, and reproducibility in EGFP detection, were obtained using frozen sections after a slow tissue-freezing protocol developed in the present study. After slow tissue freezing, specimens of testis and epididymis could be stored at -70 degrees C for at least six weeks without any affect on EGFP fluorescence. Hence, the method developed offers the possibility to analyze EGFP fluorescence in tissues several weeks after specimen collection. The sensitivity achieved was equal to that found in immunohistochemistry, applying biotin-streptavidin-FITC detection. Confocal microscopy is known to have the advantage that fluorescence can be detected from cells in different layers. This was found to be important as regards detecting EGFP fluorescence because the fluorescence was destroyed at the cut surfaces of sections produced by either vibratome or cryomicrotome.
Escherichia coli heat‐labile enterotoxin B subunit prevents autoimmune arthritis through induction of regulatory CD4+ T cells (2002)

Mucosal administration of EtxB can be used to prevent or treat CIA. Modulation of the anti-CII immune response by EtxB is associated with a reduction in Th1 cell reactivity without a concomitant shift toward Th2. Instead, EtxB mediates its effects through enhancing the activity of a population of CD4+ regulatory T cells.
Phenol, A Potent Stimulator of Adenylate Cyclase in Human Thyroid Membranes (1981)

Among several commercial hCG preparations tested for their ability to stimulate adenylate cyclase in a human thyroid particulate fraction, only a pharmaceutical preparation (APL) was active. Activity of this preparation was lost during dialysis, but could be restored fully by the addition of phenol and partially by the addition of benzyl alcohol, the two additives present in APL. Phenol itself (0.040 - 2.0 mg/ml) induced a potent, dose-dependent stimulation of adenylate cyclase activity in a human thyroid particulate fraction and was also active in plasma membranes from rat liver and kidney cortex. Phenol exerted a biphasic effect on [125I]-bTSH binding to human thyroid membranes. Concentrations between 0.33 and 3.3 mg/ml were stimulatory to binding, while higher concentrations were inhibitory.
Effects of collagen type on the behavior of adult canine annulus fibrosus cells in collagen–glycosaminoglycan scaffolds (2004)

The healing of intervertebral disc defects may be improved by the implantation of cell-seeded collagen-based scaffolds. The present study evaluated in vitro the effects of the collagen type (type I vs type II) from which the scaffolds were fabricated on the behavior of adult canine annulus fibrosus cell-seeded collagen-glycosaminoglycan (GAG) scaffolds. Protein and GAG biosynthesis continued through the 8-week period of the experiment, demonstrating the viability of the cells in type I and type II collagen-GAG scaffolds. Statistical analysis revealed no significant effect of the type of collagen that makes up the scaffold on the biosynthetic activity. For both scaffold types, the amount of retained newly synthesized proteins increased from 1 to 2 weeks and from 6 to the 8 weeks. In contrast, the rate of GAG retention increased to a maximum at 4 weeks for both types of scaffolds, then decreased to about 50% of that level after 8 weeks. The number of cells generally increased the first week but then decreased in type I scaffolds while remaining constant in type II scaffolds. It could be assumed that most newly synthesized protein was lost to the medium, as the quantity of protein and collagen remained constant. Cell-mediated contraction of the scaffolds contributed to folds that formed in the constructs and to create an oriented architecture tissue. These findings commend the use of a type II collagen-GAG scaffold for further study on the basis of its maintenance of cell number and the slightly higher accumulated GAG content.
Comparison of scores for bimodality of gene expression distributions and genome-wide evaluation of the prognostic relevance of high-scoring genes (2010)

Genes with high bimodality scores are promising candidates for defining prognostic patient subgroups from expression data. We discuss advantages and disadvantages of the different scores for prognostic purposes. The outlier-sum statistic may be particularly valuable for the identification of genes to be included in prognostic signatures. Among the genes identified as bimodal in the breast cancer data set several have not yet previously been recognized to be prognostic and bimodally expressed in breast cancer.
Ordered mesoporous metal oxides: synthesis and applications (2012)

Great progress has been made in the preparation and application of ordered mesoporous metal oxides during the past decade. However, the applications of these novel and interesting materials have not been reviewed comprehensively in the literature. In the current review we first describe different methods for the preparation of ordered mesoporous metal oxides; we then review their applications in energy conversion and storage, catalysis, sensing, adsorption and separation. The correlations between the textural properties of ordered mesoporous metal oxides and their specific performance are highlighted in different examples, including the rate of Li intercalation, sensing, and the magnetic properties. These results demonstrate that the mesoporosity has a direct impact on the properties and potential applications of such materials. Although the scope of the current review is limited to ordered mesoporous metal oxides, we believe that the information may be useful for those working in a number of fields.
Interactive effects of PTH and mechanical stress on nitric oxide and PGE2production by primary mouse osteoblastic cells (2003)

Parathyroid hormone (PTH) and mechanical stress both stimulate bone formation but have opposite effects on bone resorption. PTH increased loading-induced bone formation in a rat model, suggesting that there is an interaction of these stimuli, possibly at the cellular level. To investigate whether PTH can modulate mechanotransduction by bone cells, we examined the effect of 10-9 M human PTH-(1-34) on fluid flow-induced prostaglandin E2 (PGE2) and nitric oxide (NO) production by primary mouse osteoblastic cells in vitro. Mechanical stress applied by means of a pulsating fluid flow (PFF; 0.6 +/- 0.3 Pa at 5 Hz) stimulated both NO and PGE2 production twofold. In the absence of stress, PTH also caused a twofold increase in PGE2 production, but NO release was not affected and remained low. Simultaneous application of PFF and PTH nullified the stimulating effect of PFF on NO production, whereas PGE2 production was again stimulated only twofold. Treatment with PTH alone reduced NO synthase (NOS) enzyme activity to undetectable levels. We speculate that PTH prevents stress-induced NO production via the inhibition of NOS, which will also inhibit the NO-mediated upregulation of PGE2 by stress, leaving only the NO-independent PGE2 upregulation by PTH. These results suggest that mechanical loading and PTH interact at the level of mechanotransduction.
Substituent groups linked by alkali‐labile bonds to arabinose and xylose residues of legume, grass and cereal straw cell walls and their fate during digestion by rumen microorganisms (1983)

Abstract The distribution of alkali labile substituents of the neutral sugar components of hemicellulose in unfractionated cell walls of early‐ and late‐cut perennial ryegrass, wheat and barley straw, and white clover, before and after extended incubation in the rumen, was determined by a modified methylation technique. Xylose residues were found to be extensively substituted, with 50% of residues in the Gramineae and 75% in white clover carrying substituent groups on O ‐2 and/or O ‐3. Acetyl groups could account for 50–70% of substitutions, the remainder being to unknown cell wall components. The distribution of alkali‐labile substituents of xylose was the same in the original plant material as in residues recovered from the rumen, and was not affected by delignification under conditions which preserved the acetyl content of cell walls. Arabinose residues were heavily substituted at O ‐5, with 40–60 % of residues from the Gramineae, but only 10% of residues from the white clover, carrying substituent groups at this site. Linkages to O ‐5 of arabinose were preserved during digestion and accumulated in residues recovered from the rumen. In all plants examined, the extent of O ‐5 substitution strongly correlated with the proportion of total phenolics ( r =0.844) and total phenolics minus phenolic acids ( r =0.779) present. The correlation was improved when restricted to the Gramineae ( r =0.879 and 0.881 respectively). Within the Gramineae, the increase in the extent of substitution to O ‐5 of arabinose correlated well with the increase in the proportion of total material in digested residues ( r =0.899). As correlations were retained or improved when values for phenolic acids were subtracted from total phenolics, and as the proportion of phenolic acids decreased during digestion, it is suggested that linkages to O ‐5 of arabinose represent one form of lignin‐carbohydrate bonding. The importance of such linkages to the control of polysaccharide degradation and the effect of their cleavage by alkali‐treatment is discussed.
Metastatic potential of SP1 mouse mammary adenocarcinoma cells is differentially induced by activated and normal forms of c-H-ras. (1987)

The mouse mammary adenocarcinoma cell line SP1 was transfected with either the activated T24-H-ras or the normal c-H-ras gene and assessed for metastatic potential in syngeneic CBA/J or nude mice. Unlike the parental control cells, which were tumorigenic but unable to metastasize from a subcutaneous site, all SP1 transfectants expressing the T24-H-ras gene were able to metastasize (predominantly to the lung). In contrast, a much smaller fraction of the clones obtained following transfection with either normal c-H-ras or pSV2neo were metastatic and, significantly, elevated expression of the c-H-ras proto-oncogene did not correlate with acquisition of metastatic potential. We conclude that activated and normal forms of the c-H-ras gene differ in their ability to confer metastatic potential to SP1 mouse mammary adenocarcinoma cells.
Environmentally safe approaches to crop disease control (1998)

Environmental Aspects The Influence of Environment on the Development and Control of Disease, H.A. McCartney Ecological Approaches to Disease Control, M.A. Boudreau and C.C. Mundt Chemical Control Use of Chemical Measures, R.A. Hamlen, B. Labit, J.A. Bruhn, M.J. Holliday, C.M. Smith, and C.A. Shillingford Biological Control Bacteria for Biological Control of Plant Diseases, P.A. Backman, M. Wilson, and J.F. Murphy Fungal Control Agents, R.S. Mehrotra, K.R. Aneja, and A. Aggarwal Viral Control Agents, C.M. Rush and J.L. Sherwood Physiological Aspects Constitutive Barriers and Plant Disease Control, D. Prusky Induced Resistance to Disease, R. Hammerschmidt and E.K. Dann Plant Breeding, M. Carson Cultural Practices Sanitation, Eradication, Exclusion, and Quarantine, A.B. Gould and B. I. Hillman Agronomic Measures, C.M. Rush, G. Piccinni, and R.M. Harveson Physical Methods of Soil Sterilization for Disease Management, Including Soil Solarization, R.J. McGovern and R. McSorley Biotechnology Tissue Culture, J.M. Van Eck and F.D. Smith Genetic Engineering, M. Fuchs and D. Gonsalves Index