gebhart/patrepeval huggingface dataset:
Clinical comparability of marketed formulations of botulinum toxin (2004)

The majority of pharmaceutical products are patented in early phases of their discovery to preclude competition by similar products. Due to unusual circumstances (botulinum toxin is an unpatentable natural product and it is considered to be a biological weapon), technology know-how for botulinum toxin production was classified rather then available in the scientific community. Botulinum toxin type A was marketed in two pharmaceutical distinct formulations from competitor companies. Serendipity proved that the two formulations were not equipotent in terms of mouse units. From a regulatory point of view, differences in potency of distinct formulations are not a matter of concern because each formulation is licensed based on its own set of data. As far as the data in each case is sufficient to prove that a particular formulation is safe and efficacious at its defined dosage, a license for use can be granted. On the other hand, generation of data on comparability is the only way that clinicians and managers can ascertain which product (formulation, serotype) is most cost-effectiveness and to determine whether there are relevant differences in their safety profiles. The results of the systematic review of head-to-head randomised trials comparing BOTOX to Dysport suggest that the two formulations are not bioequivalent whatever the dose relationship. Data on comparative immunogenicity are not available. The indirect comparison of the results obtained in randomised clinical trials comparing BOTOX to placebo and Dysport to placebo support that intrinsic differences are present in the two products. It is concluded that comparative economic evaluations of different botulinum toxin formulations should move away from cost-minimization approaches based on the presumption of bioequivalence and move toward cost-effectiveness or cost-utility models.
Synthesis and Single‐Particle Optical Detection of Low‐Polydispersity Plasmonic‐Superparamagnetic Nanoparticles (2008)

The synthesis, magnetic characterization, and optical properties of nanoparticles with iron oxide cores and gold shells are presented. The nanoparticles are superparamagnetic at room temperature and can be reversibly collected by a permanent magnet. They display a localized surface plasmon resonance peak at 605 nm, and their large scattering cross-section allows them to be individually resolved in darkfield optical microscopy as they undergo Brownian motion in aqueous suspension. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2089/2008/adma200702196_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.
Synthesis of a carboxamide linked T*T dimer and its incorporation in oligonucleotides (1993)

The condensation of 5'-O-protected 3'-O-(2-aminoethyl)thymidine with 1,2-dideoxy-1-thyminyl-beta-D-erythro-pentofuranuronic acid gives a T*T dimer with * representing a 3'-OCH2CH2NHC(O)-4' linkage connecting the two pentofuranosyl moieties. The incorporation of this dimer in oligonucleotide sequences show only moderately lowered Tm values when hybridized with a complementary DNA relative to the unmodified DNA duplex. Consistently, no looped-out or bubble-type structure could be detected in DNA duplexes with an internal T*T module. Moreover, the 5-atom carboxamide linker causes complete stop on DNA polymerization and on exonuclease III degradation.
Damage to Coal Permeability During Hydraulic Fracturing (1991)

ABSTRACT Coalbed methane wells are routinely fracture stimulated using gelled fluids and proppants. Surprisingly, there is no published report on the compatibility of the coals with fracturing fluids containing polymers, surfactants, biocides, friction reducers, and other chemicals. The objective of the research presented here was to understand and measure the change in coal permeability after it was brought in contact with hydraulic fracturing fluids. The permeabilities of whole core samples of coals from San Juan and Warrior Basins were severely damaged (5-10 fold reduction) after they were exposed to gelled fracturing fluids that had been broken and filtered repeatedly. Efforts to restore coal permeability by prolonged flushing with water and HC1/HF solutions were unsuccessful. While damage to coal permeability appears to have been caused by sorption-induced swelling of the coal matrix, some plugging of the cleat system by residual gels cannot be ruled out. Based on limited lab data, it appears that even water containing low concentrations of friction reducing polymers can cause significant damage to coal permeability. These results are alarming since extensive damage to coal permeability by gelled fluids and friction reducing polymers could negate most of the benefits of a large effective wellbore radius created during an expensive fracture stimulation. Field comparison of well productivities suggest that, in general, small low cost propped water fractures are as effective, if not more, as large high cost propped gel fractures. It is anticipated that coal permeability damage would be exacerbated in thin, low cleat porosity, high permeability coal seams. It is recommended that every effort be made to avoid contacting coals with gelled fluids, polymers, or liquid chemicals. Furthermore, remedial workover treatment should be considered for coal wells that could have been damaged in the past by hydraulic fracture stimulation.
Differential induction of four msx homeobox genes during fin development and regeneration in zebrafish (1995)

To study the genetic regulation of growth control and pattern formation during fin development and regeneration, we have analysed the expression of four homeobox genes, msxA, msxB, msxC and msxD in zebrafish fins. The median fin fold, which gives rise to the unpaired fins, expresses these four msx genes during development. Transcripts of the genes are also present in cells of the presumptive pectoral fin buds. The most distal cells, the apical ectodermal ridge of the paired fins and the cleft and flanking cells of the median fin fold express all these msx genes with the exception of msxC. Mesenchymal cells underlying the most distal cells express all four genes. Expression of the msx genes in the fin fold and fin buds is transient and, by 3 days after fertilization, msx expression in the median fin fold falls below levels detectable by in situ hybridization. Although the fins of adult zebrafish normally have levels of msx transcripts undetectable by in situ hybridization, expression of all four genes is strongly reinduced during regeneration of both paired and unpaired fins. Induction of msx gene expression in regenerating caudal fins occurs as early as 30 hours postamputation. As the blastema forms, the levels of expression increase and reach a maximum between the third and fifth days. Then, msx expression progressively declines and disappears by day 12 when the caudal fin has grown back to its normal size. In the regenerating fin, the blastema cells that develop at the tip of each fin ray express msxB and msxC. Cells of the overlying epithelium express msxA and msxD, but do not express msxB or msxC. Amputations at various levels along the proximodistal axis of the fin suggest that msxB expression depends upon the position of the blastema, with cells of the rapidly proliferating proximal blastema expressing higher levels than the cells of the less rapidly proliferating distal blastema. Expression of msxC and msxD is independent of the position of the blastema cell along this axis. Our results suggest distinct roles for each of the four msx genes during fin development and regeneration and differential regulation of their expression.
Interferon-induced inhibition of protein synthesis in L-cell extracts: an ATP-dependent step in the activation of an inhibitor by double-stranded RNA. (1976)

The translation of encephalomyocarditis virion RNA in extracts from interferon-treated L-cells is inhibited by the addition of double-stranded RNA (dsRNA) at 400 ng/ml. A similar inhibition in response to dsRNA is seen in control cell extracts supplemented with small amounts of a postribosomal supernatant fraction from interferon-treated cells (interferon cell sap): Neither interferon cell sap nor dsRNA alone is inhibitory in control systems. The inhibition is much reduced if translation is carried out at low ATP concentrations.Conversely, the inhibitory capacity of the interferon cell sap is increased 100-fold if it is preincubated with dsRNA and ATP prior to its addition to the protein-synthesizing system. After this preincubation all detectable dsRNA can be removed without any diminution of the inhibitory activity of the cell sap. These results are compatible with a two-step model for the inhibition in which a pre-inhibitor is activated by dsRNA, the activated inhibitor then interacting with the protein synthesis system to inhibit translation.
Molecular Pathways Involved in Prostate Carcinogenesis: Insights from Public Microarray Datasets (2012)

This study illustrates how a standardized bioinformatics evaluation of existing microarray data and subsequent pathway analysis can quickly and cost-effectively provide essential information about important molecular pathways and cellular processes involved in prostate cancer development and disease progression. The presented results may assist in biomarker profiling and the development of novel treatment approaches.
ExploringLactobacillus plantarumGenome Diversity by Using Microarrays (2005)

Lactobacillus plantarum is a versatile and flexible species that is encountered in a variety of niches and can utilize a broad range of fermentable carbon sources. To assess if this versatility is linked to a variable gene pool, microarrays containing a subset of small genomic fragments of L. plantarum strain WCFS1 were used to perform stringent genotyping of 20 strains of L. plantarum from various sources. The gene categories with the most genes conserved in all strains were those involved in biosynthesis or degradation of structural compounds like proteins, lipids, and DNA. Conversely, genes involved in sugar transport and catabolism were highly variable between strains. Moreover, besides the obvious regions of variance, like prophages, other regions varied between the strains, including regions encoding plantaricin biosynthesis, nonribosomal peptide biosynthesis, and exopolysaccharide biosynthesis. In many cases, these variable regions colocalized with regions of unusual base composition. Two large regions of flexibility were identified between 2.70 and 2.85 and 3.10 and 3.29 Mb of the WCFS1 chromosome, the latter being close to the origin of replication. The majority of genes encoded in these variable regions are involved in sugar metabolism. This functional overrepresentation and the unusual base composition of these regions led to the hypothesis that they represented lifestyle adaptation regions in L. plantarum. The present study consolidates this hypothesis by showing that there is a high degree of gene content variation among L. plantarum strains in genes located in these regions of the WCFS1 genome. Interestingly, based on our genotyping data L. plantarum strains clustered into two clearly distinguishable groups, which coincided with an earlier proposed subdivision of this species based on conventional methods.
T cell subsets defined by expression of Lyt-1,2,3 and Thy-1 antigens. Two-parameter immunofluorescence and cytotoxicity analysis with monoclonal antibodies modifies current views. (1980)

Using monoclonal antibodies and multiparameter fluorescence analyses, we show that the expression of Lyt-1, Lyt-2, and Lyt-3 on T cell subpopulations is more complex than was originally recognized by the cytotoxic depletion studies with conventional reagents that defined the Lyt-1+2+3+, Lyt-1+2-3-, and Lyt-1-2+3+ populations. We detect at least some Lyt-1 on all T (Thy-1-bearing) lymphocytes; however, in agreement with previous studies, we find that Lyt-2+3+ cells are more difficult to depelete with anti-Lyt-1 than Lyt-1+2-3- cells. Surprisingly, we found a small subpopulation of cells carrying relatively large amounts of Lyt-1 and no Thy-1 detectable by fluorescence-activated cell sorter analysis. We also detect cells with this phenotype histologically in B cell zones (primary follicles) and germinal centers in spleen and lymph nodes. In general, the Lyt-1 only population represents approximately 2% of spleen cells. The relative quantitative expression of Thy-1, Lyt-1, Lyt-2, and Lyt-3 changes systematically during T cell maturation. Among Lyt-1+2+3+ cells in the thymus, Thy-1 and Lyt-2 are high, whereas Lyt-1 is low. Among splenic T cells, in contrast, Thy-1 is low, Lyt-1 is high, and Lyt-2 and Lyt-3 are a little higher than in thymus. In general, Thy-1 expression is negatively correlated with Lyt-1. Thus, even among splenic and lymph node T cells subpopulations exist that tend to be either high Thy-1 and low Lyt-1 or vice versa. Lyt-2+3+ cells represent approximately 85% of thymocytes but only approximately 35% of splenic or lymph node T cells. The Lyt-2+3+ cells are found predominantly in the low Lyt-1, high Thy-1 subpopulation.
Baff and Rheumatic Autoimmune Disorders: Implications for Disease Management and Therapy (2007)

Interest in B-cells has been revived due to the description of new functions. Supporting a role for B-cells in the genesis of autoimmune diseases is the fact that the B-cell activating factor of the TNF ligand family (BAFF) is essential in their physiology. However, in each disease, this is restricted to a subgroup of patients. Based on experiments in mice, and validated in humans, this new cytokine has been highlighted. Excessive production of BAFF alters immune tolerance by rescuing self-binding B-cells. Overexpression in mice leads to autoimmune manifestation, and BAFF levels are elevated in the serum of autoimmune patients. Similar abnormalities occur in chronic lymphocytic leukemia. Recent works suggest that antagonizing the protein (or competing for its receptors) is relevant to the treatment. Advances in our understanding of the BAFF system offers the opportunity to improve our therapeutic approach.
The Weak Link: Optimization of the Ligand–Nanoparticle Interface To Enhance Cancer Cell Targeting by Polymer Micelles (2017)

Many promising targeting ligands are hydrophobic peptides, and these ligands often show limited accessibility to receptors, resulting in suboptimal targeting. A systematic study to elucidate the rules for the design of linkers that optimize their presentation on nanoparticles has not been carried out to date. In this study, we recombinantly synthesized an elastin-like polypeptide diblock copolymer (ELP<sub>BC</sub>) that self-assembles into monodisperse micelles. AHNP and EC1, two hydrophobic ErbB2-targeted peptide ligands, were incorporated at the C-terminus of the ELP<sub>BC</sub> with an intervening peptide linker. We tested more than 20 designs of peptide linkers, where the linker could be precisely engineered at the gene level to systematically investigate the molecular parameters-sequence, length, and charge-of the peptide linker that optimally assist ligands in targeting the ErbB2 receptor on cancer cells. We found that peptide linkers with a minimal length of 12 hydrophilic amino acids and an overall cationic charge-and that impart a zeta potential of the micelle that is close to neutral-were necessary to enhance the uptake of peptide-modified ELP<sub>BC</sub> micelles by cancer cells that overexpress the ErbB2 receptor. This work advances our understanding of the optimal presentation of hydrophobic ligands by nanoparticles and suggests design rules for peptide linkers for targeted delivery by polymer micelles, an emerging class of nanoparticle carriers for drugs and imaging agents.
Increasing and decreasing protein stability: Effects of revertant substitutions on the thermal denaturation of phage λ repressor (1985)

The thermal denaturations of five revertant lambda repressors containing single amino acid substitutions in their N-terminal domains have been studied by differential scanning calorimetry. Two substitutions slightly decrease stability, and the remaining three render the protein more stable than wild type. The Gly48----Asn and Gly48----Ser proteins are 4 degrees C more stable than wild type. These two substitutions replace an alpha helical residue, and in each case a poor helix forming residue, glycine, is replaced by a residue with a higher helical propensity. We also present data showing that one revertant, Tyr22----Phe, has reduced operator DNA binding affinity despite its enhanced stability.
Internalization and cycling of the T cell antigen receptor. Role of protein kinase C. (1987)

The dynamics of the T cell antigen receptor on a murine antigen specific T cell hybridoma have been analyzed using a monoclonal anti-receptor antibody. When this antibody, A2B4-2, is bound to surface receptors, no internalization is seen at 4 degrees C. Upon warming to 37 degrees C, between 20 and 30% of the antibody molecules are internalized over 20-30 min as measured by sensitivity to external acid. This level of internalization is identical if monovalent Fab fragments are used. In contrast, cross-linking of the anti-receptor antibody with a second antibody leads to rapid internalization of 100% of prebound surface A2B4-2. Phorbol 12-myristate 13-acetate (PMA) leads to the rapid internalization of up to 65% of the surface A2B4-2 or A2B4-2 Fab fragments. This effect requires protein kinase C and can be completely inhibited by depleting this kinase from the cells by long term treatment with high doses of PMA. Pretreatment of the T cells with PMA leads to a 40-50% drop in surface T cell antigen receptor expression. Despite the loss of surface receptors, the uptake of A2B4-2 in PMA-treated cells at 37 degrees C is identical to that seen in control cells. The total uptake of A2B4-2 at 37 degrees C is 25-30% greater than the number of surface receptors in control cells and about 100-150% greater than the number of surface receptors in PMA-treated cells. At steady state the percentage of total A2B4-2 on the cell surface is 75% for control cells and 38% for PMA-treated cells. The good agreement of these numbers with the percent internalization of a cohort of surface receptors suggests that all receptors are constantly cycling. The effect of PMA is to alter the kinetic parameters of this cycling, thus changing the steady state distribution of receptors between the plasma membrane and internal, presumably endosomal compartments. Measurement of initial rates of internalization suggests that the PMA effect can be largely explained by an increase in the internalization rate constant.
Vitamin K dependent carboxylase: subcellular location of the carboxylase and enzymes involved in Vitamin K metabolism in rat liver (1980)

Vitamin K dependent carboxylation of an exogenous peptide substrate and endogenous protein substrates, vitamin K epoxidation, and reduction of vitamin K epoxide were measured in subcellular fractions from rat liver. The rough microsomal fraction was highly enriched in all four activities; lower levels were found in smooth microsomes. Mitochondria, nuclei, and cytosol had negligible activities. The addition of 0.2% Triton X-100 to intact microsomes resulted in a 10-20-fold stimulation in carboxylation of a peptide substrate. This marked latency suggests that the active site of the carboxylase may be accessible only from the lumen of the microsomal membrane. A lumen-facing orientation of the carboxylase was also supported by its inaccessibility to trypsin in intact microsomes contrasted with marked inhibition by trypsin in detergent-permeabilized microsomes. Vitamin K epoxidase and epoxide reductase activities were also inhibited by trypsin much more effectively in permeabilized than in intact microsomes, although some degree of exposure at the cytosolic surface was also indicated. These data suggest that carboxylation is an early event in prothrombin synthesis occurring primarily on the lumen side of the rough endoplasmic reticulum membrane. The location of the vitamin K epoxidation-reduction cycle enzymes is consistent with their possible role in the carboxylation reaction.
Adaptive Multiple Subtraction with Non-Stationary Helical Shaping Filters (2001)

P 167 ADAPTIVE MULTIPLE SUBTRACTION WITH NON-STATIONARY HELICAL SHAPING FILTERS 1 SUMMARY JAMES RICKETT ANTOINE GUITTON AND DOUGLAS GRATWICK Department of Geophysics Stanford University Stanford CA 94305 USA We suppress surface-related multiples with a smart adaptive least-squares subtraction scheme in the time-space domain after modelling multiples with a very fast but approximate modelling algorithm. The subtraction scheme is based on using a linear solver to estimate a damped non-stationary shaping filter. Convergence is improved by the preconditioning with a space domain helical roughening filter. Dragoset and Jeričević (1998) describe a two-step multiple elimination process: prediction followed by subtraction with an
Pathogenic Neisseria Trigger Expression of Their Carcinoembryonic Antigen-related Cellular Adhesion Molecule 1 (CEACAM1; Previously CD66a) Receptor on Primary Endothelial Cells by Activating the Immediate Early Response Transcription Factor, Nuclear Factor-κB (2001)

Neisseria gonorrhoeae express opacity-associated (Opa) protein adhesins that mediate binding to various members of the carcinoembryonic antigen-related cellular adhesion molecule (CEACAM; previously CD66) receptor family. Although human umbilical vein endothelial cells express little CEACAM receptor in vitro, we found neisserial infection to induce expression of CEACAM1, CEACAM1-3L, and CECAM1-4L splice variants. This mediates an increased Opa(52)-dependent binding of gonococci by these cells. The induced receptor expression did not require bacterial Opa expression, but it was more rapid with adherent bacteria. Because the time course of induction was similar to that seen for induced proinflammatory cytokines, we tested whether CEACAM1 expression could be controlled by a similar mechanism. Gonococcal infection activated a nuclear factor-kappaB (NF-kappaB) heterodimer consisting of p50 and p65, and inhibitors that prevent the nuclear translocation of activated NF-kappaB complex inhibited CEACAM1 transcript expression. Each of these effects could be mimicked by using culture filtrates or purified lipopolysaccharide instead of intact bacteria. Together, our results support a model whereby the outer membrane "blebs" that are actively released by gonococci trigger a Toll-like receptor-4-dependent activation of NF-kappaB, which up-regulates the expression of CEACAM1 to allow Opa(52)-mediated neisserial binding. The regulation of CEACAM1 expression by NF-kappaB also implies a broader role for this receptor in the general inflammatory response to infection.
Unique aspects of distribution system harmonics due to high impedance ground faults (1990)

The effects of the many sources of harmonics which occur on distribution systems are discussed and contrasted with the single source of harmonics from a high-impedance ground fault. Field data are presented which show the complexity of modeling the ambient harmonics and the simplicity of the change in the phasor value of the third harmonic which occurs due to a high-impedance ground fault. This phasor change is shown to be unique and predictable and hence suitable for use in detecting these faults. It is shown that variations in ambient harmonics may be greater than the change due to a high-impedance ground fault and must be considered in the fault detection system. Calculations of fault current harmonics are simpler than those for the ambient harmonics.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>