gebhart/patrepeval huggingface dataset:
Three-Dimensional Starch Model for Simulation of Corrective Osteotomy for a Complex Bone Deformity: A Case Report (2003)

The complex valgus deformity of the right ankle of a 24-year-old Maffucci syndrome man was corrected by three-dimensional osteotomy followed by limb lengthening. Before surgical correction of the deformity, we used computed tomography data to make a life-size three-dimensional plastic model of the deformed ankle for an accurate understanding of the anatomical deformity. We then used this model to perform a simulated osteotomy. The real osteotomy was performed immediately afterwards and valgus and recurvatum deformities were corrected accurately. We recommend simulated surgery using a three-dimensional plastic model which will improve the pre-operative planning technique and the accuracy of the end results.
Activation of (R)-2-hydroxyglutaryl-CoA Dehydratase from Acidaminococcus fermentans (1995)

(R)-2-Hydroxyglutaryl-CoA dehydratase (HgdAB) from Acidaminococcus fermentans catalyses the reversible dehydration of its substrate to glutaconyl-CoA. The enzyme has to be activated by ATP, MgCl2, and Ti(III)citrate by an activator protein (HgdC) that is present in the organism at very low concentrations. Cell-free extracts of a recombinant Escherichia coli strain, in which hgdC was expressed, contained the activator with a specific activity of up to 45 U'/mg protein (1 U' is the amount of activator required to generate 1 U dehydratase activity under standard assay conditions). The recombinant protein was purified 44-fold to a specific activity of 2000 U'/mg. It is a homodimer (gamma 2, 54 kDa) and contains 4 mol non-heme iron and 3 mol inorganic sulfur. Under air, the activator has a half-life of seconds and even under strict anaerobic conditions it is very unstable. The amino acid sequence of the activator shows similarities to the ATP-binding motifs of several kinases. The dehydratase component was purified from its natural source revealing a heterodimer (alpha beta, 100 kDa) that contains 4 mol non-heme iron, 4 mol inorganic sulfur, 0.3 mol riboflavin, and 1 mol FMN. A mechanism is proposed in which an iron-sulfur cluster or a flavin donates one electron to the thiolester of the substrate (R)-2-hydroxyglutaryl-CoA. The resulting ketyl may eliminate the adjacent hydroxyl group yielding an enoxy radical from which the beta-hydrogen is abstracted as a proton leading to the ketyl of glutaconyl-CoA. In the final step, the latter is oxidized to the product, whereby the reduced enzyme is regenerated. It is suggested that during the activation step, the electron of this cycle is fed into the enzyme by Ti(III)citrate and energized by hydrolysis of ATP; both functions are apparently catalysed by the activator. The enzyme remains in this activated state for several turnovers, which may explain the requirement of only catalytic amounts of ATP and substoichiometric amounts of activator (dehydratase/activator ratio approximately 200:1). The oxidants 4-nitrobenzoate, 2-nitrophenol, 3-nitrophenol, 4-nitrophenol, carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone or chloramphenicol (all at concentrations greater than or equal to 1 microM) may trap this electron resulting in a reversible, transient inactivation of the dehydratase.
Gas6/Axl Signaling Activates the Phosphatidylinositol 3-Kinase/Akt1 Survival Pathway to Protect Oligodendrocytes from Tumor Necrosis Factorα-Induced Apoptosis (2006)

Growth arrest-specific protein 6 (gas6) activity is mediated through the receptor tyrosine kinase family members Axl, Rse, and Mer, all of which are expressed in human oligodendrocytes. In this study, we examined whether recombinant human (rh) gas6 protects oligodendrocytes from growth factor (insulin) withdrawal or tumor necrosis factor-alpha (TNFalpha) cytotoxicity. In addition, we examined whether the effect was caspase-dependent, which receptor mediated the protective effect, and whether survival required Akt1 activation. Oligodendrocyte viability was assessed by O4 staining and terminal deoxynucleotidyl transferase-mediated biotinylated UTP nick end labeling. Addition of rhgas6 to insulin-depleted cultures resulted in a significant increase in oligodendrocyte viability. Rhgas6 and caspase inhibitors also reduced active caspase-3 immunoreactivity relative to TNFalpha-only-treated cultures. In cultures treated with TNFalpha (100 ng/ml), the oligodendrocyte survival rate was 18% compared with cultures treated with TNFalpha and rhgas6 (64%) or the caspase inhibitors IETD-fmk [z-Ile-Glu(OMe)-Thr-Asp(OMe)-fluoromethyl ketone] (65%) and zVAD-fmk (N-benzyloxycarbonyl-Val-Ala-Asp-fluoromethyl ketone) (63%). Increased phosphoAkt (Ser473) immunoreactivity was detected 15 min after administration of gas6 and TNFalpha to oligodendrocyte cultures but not in TNFalpha-treated cultures. The gas6 protective effect was abrogated by the Axl decoy receptor Axl-Fc, by the phosphatidylinositol 3 (PI3) kinase inhibitor LY294002 [2-(4-morpholinyl)-8-phenyl-1(4H)-benzopyran-4-one], and in Akt1(-/-) oligodendrocytes. Oligodendrocyte cultures established from wild-type and Rse(-/-) mice, but not from Axl(-/-) mice, were also protected from TNFalpha-induced cell death when maintained in rhgas6. We conclude that gas6 signaling through the Axl receptor and the PI3 kinase/Akt1 survival pathway protects oligodendrocytes from growth factor withdrawal and TNFalpha-mediated cell death.
Shape Separation of Nanometer Gold Particles by Size-Exclusion Chromatography (1999)

The shape separations of suspended gold nanoparticles were investigated using size-exclusion chromatography. The separations in shapes were identified by examining the 3-D chromatograms obtained by employing a diode-array detection system and were further confirmed by analyzing TEM images of fractional collection of particles. This shape separation was achieved by adding a mixed-surfactant system containing sodium dodecyl sulfate and poluoxyethylene (23) dodecanol (Brij-35) into the eluent, which apparently affects the adsorption behaviors of both rodlike and spherical Au nanoparticles onto the column packing materials. While the overall particle gross sizes of these two shapes were similar, the baseline resolution was unfortunately not obtainable. However, the absorption spectra from the diode-array detector could be utilized to interpret the shapes of Au nanoparticles. The potential capability for the size separation of Au nanoparticles by size-exclusion chromatography with diode-array detection was also demonstrated.
Diagnosing small bowel Crohn’s disease with wireless capsule endoscopy (2003)

Wireless capsule endoscopy diagnosed CD of the small bowel (diagnostic yield of 71%). It was demonstrated as being an effective modality for diagnosing patients with suspected CD undetected by conventional diagnostic methodologies.
Buffering and caching in large-scale video servers (2002)

Video-on-demand servers are characterized by stringent real-time constraints, as each stream requires isochronous data playout. The capacity of the system depends on the acceptable jitter per stream (the number of data blocks that do not meet their real-time constraints). Per-stream read-ahead buffering avoids the disruption in playback caused by variations in disk access time and queuing delays. With heavily skewed access patterns to the stored video data, the system is often disk arm-bound. In such cases, serving video streams from a memory cache can result in a substantial reduction in server cost. In this paper, we study the cost-performance trade-offs of various buffering and caching strategies that can be used in a large-scale video server. We first study the cost impact of varying the buffer size, disk utilization and the disk characteristics on the overall capacity of the system. Subsequently, we study the cost-effectiveness of a technique for memory caching across streams that exploits temporal locality and workload fluctuations.
Electrostatic induction of the electric field into free-flow electrophoresis devices (2006)

The electrostatic induction of an applied voltage causes electrophoretic separation under free-flow conditions and no electrolysis or electric current flowing between the metal electrodes was observed.
New drugs for migraine (2009)

After the triptans, a calcitonin gene-related peptide blocker (telcagepant) is the first acute medicine that has been developed primarily for treatment of acute migraine. Otherwise, the new drugs have been developed first for other purposes, like anticonvulsants, antihypertensives and antidepressants used for migraine prophylaxis. For acute attacks, a new way to administer a traditional drug like dihydroergotamine is under way, and documentation of efficacy in migraine has been gained for some commonly used painkillers and anti-inflammatory drugs, and for some herbal extracts. Based on insights into the basic pathophysiological mechanisms of the disorder, some drugs have been developed which seem promising in early phase II studies (NOS inhibitors and 5HT1F-receptor agonists). In the future, development and enhancements of existing medicines must be accompanied by increased efforts to develop truly new migraine drugs based on knowledge of the pathophysiology if one wishes to reduce substantially the great burden migraine poses on patients and society.
Recombinant secretory IgA for immune intervention against mucosal pathogens (1997)

Conference Article| May 01 1997 Recombinant secretory IgA for immune intervention against mucosal pathogens B. Corthésy B. Corthésy 1Swiss Institute for Experimental Cancer Research, Chemin des Boveresses 155, CH-1066 Epalinges, Switzerland Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1997) 25 (2): 471–475. https://doi.org/10.1042/bst0250471 Article history Received: October 30 1996 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share MailTo Twitter LinkedIn Cite Icon Cite Get Permissions Citation B. Corthésy; Recombinant secretory IgA for immune intervention against mucosal pathogens. Biochem Soc Trans 1 May 1997; 25 (2): 471–475. doi: https://doi.org/10.1042/bst0250471 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search Keywords: antSC, recombinant antigenized SC, IgA, immunoglobulin A, IgAd, dimeric IgA, IpaB, invasin B, LPS, lipopolysaccharide, MALT, mucosa-associated lymphoid tissue, pIgR, polymeric immunoglobulin receptor, rSC, recombinant SC, SC, secretory component, sIgA, secretory IgA This content is only available as a PDF. © 1997 Biochemical Society1997 Article PDF first page preview Close Modal You do not currently have access to this content.
Studies on identification of the Different Antigens between the wild-type Blucella Strain and the Vaccine Strain by the antibody treated with affinity chromatography (2008)

Objective Establish a method to identify the different antigens between the wild-type Blucella strain and the vaccine strain by antibody treated with affinity chromatography. Methods Use carbonyl diimi-dazole (CDI)-activated Sepharose CL-4B to prepare affinity column. Add the antibody of wild-type Blucella strain M28 to the M5 antigens column, let them flow through the column, then add them to the M28 antigenscolumn, collect the antibody, do the immunoblotting assay with M28 antigens and M5 antigens respectively. Results Two specific bands showed in the immunoblotting assay between the M28 antibody and M28 anti-gens, and the bands were inexistence in the immunoblotting assay between the M28 antibody and M5 antigens. Conclusion The antibody of M28 treated with affinity chromatography could be used for identifying the different antigens between the wild-type Blucella strain and the vaccine strain.

Key words: 
Affinity chromatography;  Different antigens;  Brucella
Evaluating the Genetic Diversity of Triticale with Wheat and Rye SSR Markers (2006)

Triticale (× Triticosecale Wittmack) is becoming increasingly important in agriculture and understanding its genetic diversity is essential for its continued improvement. Simple sequence repeat (SSR) markers are highly polymorphic and widely used for genetic diversity studies. Previous genetic diversity studies using SSRs have focused on the European winter triticale gene pool. Our objective was to investigate the genetic diversity and relationships of 80 hexaploid triticale accessions representing a more global gene pool using 43 wheat ( Triticum spp.) and 14 rye ( Secale cereale L.) SSR markers. Two hundred forty‐one alleles from 57 markers were detected with an average of 4.2 alleles per locus (ranged from 2 to 11 alleles per locus). The average gene diversity was 0.54 with a range of 0.07 to 0.86. Cluster analysis grouped the 80 accessions into five clusters that were generally consistent with the available pedigree information, country of origin, growth habit, and release year. Every larger cluster, however, included lines with unrelated pedigrees, different countries of origin, growth habit, and release year, which most likely is due to germplasm exchange among breeding programs. Genetic diversity estimates of the accessions evaluated with markers from different sources were similar (0.55 and 0.53 for wheat and rye, respectively), indicating that the wheat and rye markers detected similar genetic variability in the wheat and rye genomes of triticale.
Exploitation of Deeply Buried Coalbed Methane Using Different Hydraulic Fracturing Techniques in the Piceance Basin, Colorado and San Juan Basin New Mexico (1988)

ABSTRACT This paper reports on observations of hydraulic fracturing in coal seams gained in research activities, conducted by Resource Enterprises, Inc. and sponsored by the Gas Research Institute in their Western Cretaceous Coal Seam Project. The fracture treatments span a period from 1986 through 1988 and involve activities in the Piceance and San Juan Basins. Findings resulting from this work are that hydraulic fracture designs must reflect the lithology of the bounding strata as this affects fracture height growth and fracture geometry. Where coal seams are adjacent to sandstone, diagnostics show that hydraulic fracture growth occurs in both the sandstone and the coal and fracturing pressures are less than 1.1 psi/ft. It was also demonstrated that a linear fracture fluid could be used effectively to place proppant in the coal zone if the sandstone overlies the coal. Much higher treating pressures were encountered in fracture treatments where coals were bound by shale. Diagnostics showed the fracture to be contained primarily to the coals and the high treating pressures may have resulted in part from a complex fracture geometry. Several possible reasons for this behavior are listed. High strength casing was found to be useful in accommodating the higher treating pressures and it allowed a larger treatment to be pumped where many jobs have had to be terminated prematurely when the burst strength of the tubulars was reached. Higher injection rates and the use of solid fluid loss material are recommended to create sufficient width in the complex geometry and thereby increase the likelihood of a successful treatment. Caution is advised in the use of conventional interpretations of Nolte-Smith (log net pressure vs. lot time) plots because of the abnormally high treating pressures associated with coal and the potentially-complex fracture geometry that have been observed in mineback experiments are well beyond the scope of the simple Nolte-Smith technique.
Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of apicomplexa (1997)

The reconstruction of phylogenetic history is predicated on being able to accurately establish hypotheses of character homology, which involves sequence alignment for studies based on molecular sequence data. In an empirical study investigating nucleotide sequence alignment, we inferred phylogenetic trees for 43 species of the Apicomplexa and 3 of Dinozoa based on complete small-subunit rDNA sequences, using six different multiple-alignment procedures: manual alignment based on the secondary structure of the 18S rRNA molecule, and automated similarity-based alignment algorithms using the PileUp, ClustalW, TreeAlign, MALIGN, and SAM computer programs. Trees were constructed using neighboring-joining, weighted-parsimony, and maximum-likelihood methods. All of the multiple sequence alignment procedures yielded the same basic structure for the estimate of the phylogenetic relationship among the taxa, which presumably represents the underlying phylogenetic signal. However, the placement of many of the taxa was sensitive to the alignment procedure used; and the different alignments produced trees that were on average more dissimilar from each other than did the different tree-building methods used. The multiple alignments from the different procedures varied greatly in length, but aligned sequence length was not a good predictor of the similarity of the resulting phylogenetic trees. We also systematically varied the gap weights (the relative cost of inserting a new gap into a sequence or extending an already-existing gap) for the ClustalW program, and this produced alignments that were at least as different from each other as those produced by the different alignment algorithms. Furthermore, there was no combination of gap weights that produced the same tree as that from the structure alignment, in spite of the fact that many of the alignments were similar in length to the structure alignment. We also investigated the phylogenetic information content of the helical and nonhelical regions of the rDNA, and conclude that the helical regions are the most informative. We therefore conclude that many of the literature disagreements concerning the phylogeny of the Apicomplexa are probably based on differences in sequence alignment strategies rather than differences in data or tree-building methods.
Syngeneic anti-idiotypic antisera to murine monoclonal antibodies to monomorphic and polymorphic determinants of HLA class I antigens. (1987)

BALB/c mice were immunized with syngeneic anti-HLA class I monoclonal antibodies. The latter included the anti-HLA-A2, A28 monoclonal antibody (MoAb) CR11-351, the MoAb Q6/64 to a determinant restricted to HLA-B antigens and the MoAb CR10-215 and CR11-115 to the same (or spatially close) monomorphic determinant. Anti-idiotypic antibodies could be detected in bleedings obtained 3 days after the first booster, increased in titer in bleedings obtained after the second booster, and persisted at high levels in subsequent bleedings. The four anti-HLA class I MoAb did not differ in their ability to elicit syngeneic anti-idiotypic antibodies. Cross-blocking studies with a panel of anti-HLA class I, anti-HLA class II, and anti-human melanoma-associated antigen (MAA) MoAb showed that the anti-MoAb CR10-215 and anti-MoAb CR11-115 antisera contain only antibodies to private idiotopes, whereas the anti-HLA MoAb CR11-351 and anti-MoAb Q6/64 antisera also contain antibodies to public idiotopes. The latter are expressed by the anti-HLA class I MoAb CR11-351, Q1/28, Q6/64, and 6/31, and by the anti-HLA class II MoAb Q5/6, Q5/13, 127, and 441. Public idiotopes were not detected on the nine anti-MAA MoAb tested. Public idiotopes do not interfere with the binding of anti-HLA MoAb with the corresponding antigenic determinants. On the other hand private idiotopes are located within the antigen-combining site, because anti-idiotypic antisera specifically inhibit the binding of the corresponding immunizing anti-HLA class I MoAb to cultured human lymphoid cells in a dose-dependent manner. Analysis by isoelectric focusing of the anti-HLA class I MoAb antisera showed that the spectrotype of the anti-MoAb CR11-351 antiserum comprises four components that focus in the pH 6.9 to 6.2 range, the spectrotype of anti-MoAb Q6/64 antiserum comprises three components that focus in the pH 6.5 to 6.1 range, the spectrotype of the anti-MoAb CR10-215 antiserum comprises three components that focus in the pH 6.4 to 6.1 range, and the spectrotype of the anti-MoAb CR11-115 antiserum comprises three components that focus in the pH 6.6 to 6.4 range.
Serial Intraoperative Magnetic Resonance Imaging of Brain Shift (2001)

Brain shift is a continuous dynamic process that evolves differently in distinct brain regions. Therefore, only serial imaging or continuous data acquisition can provide consistently accurate image guidance. Furthermore, only serial intraoperative magnetic resonance imaging provides an accurate basis for the computational analysis of brain deformations, which might lead to an understanding and eventual simulation of brain shift for intraoperative guidance.
The Saccharomyces cerevisiae Anaphase-Promoting Complex Interacts with Multiple Histone-Modifying Enzymes To Regulate Cell Cycle Progression (2010)

The anaphase-promoting complex (APC), a large evolutionarily conserved ubiquitin ligase complex, regulates cell cycle progression through mitosis and G(1). Here, we present data suggesting that APC-dependent cell cycle progression relies on a specific set of posttranslational histone-modifying enzymes. Multiple APC subunit mutants were impaired in total and modified histone H3 protein content. Acetylated H3K56 (H3K56(Ac)) levels were as reduced as those of total H3, indicating that loading histones with H3K56(Ac) is unaffected in APC mutants. However, under restrictive conditions, H3K9(Ac) and dimethylated H3K79 (H3K79(me2)) levels were more greatly reduced than those of total H3. In a screen for histone acetyltransferase (HAT) and histone deacetylase (HDAC) mutants that genetically interact with the apc5(CA) (chromatin assembly) mutant, we found that deletion of GCN5 or ELP3 severely hampered apc5(CA) temperature-sensitive (ts) growth. Further analyses showed that (i) the elp3Δ gcn5Δ double mutant ts defect was epistatic to that observed in apc5(CA) cells; (ii) gcn5Δ and elp3Δ mutants accumulate in mitosis; and (iii) turnover of the APC substrate Clb2 is not impaired in elp3Δ gcn5Δ cells. Increased expression of ELP3 and GCN5, as well as genes encoding the HAT Rtt109 and the chromatin assembly factors Msi1 and Asf1, suppressed apc5(CA) defects, while increased APC5 expression partially suppressed elp3Δ gcn5Δ growth defects. Finally, we demonstrate that Gcn5 is unstable during G(1) and following G(1) arrest and is stabilized in APC mutants. We present our working model in which Elp3/Gcn5 and the APC work together to facilitate passage through mitosis and G(1). To progress into S, we propose that at least Gcn5 must then be targeted for degradation in an APC-dependent fashion.