gebhart/patrepeval huggingface dataset:
Production of a novel extracellular acidic lipase from Pseudomonas gessardii using slaughterhouse waste as a substrate (2010)

An isolate exhibiting high extracellular lipolytic activity was identified as Pseudomonas gessardii by 16S rDNA gene sequence analysis. The slaughterhouse waste, goat tallow, was used as a lipid substrate for the production of acidic lipase by P. gessardii. The maximum lipase activity of 156 U/ml was observed at an acidic pH of 3.5 and at 0.31 g substrate concentration. The purification steps resulted in the isolation of acidic lipase with a specific activity of 1,473 U/mg and a molecular weight of 94 kDa. One interesting feature of this purified lipase is its stability at highly acidic pH ranging from 2.0 to 5.5 with a high molecular weight. The amino acid composition was determined using HPLC. This acidic lipase has potential applications in the medicinal field as a substitute for pancreatic lipases for enzyme therapy, oleochemical and in biotechnological industries.
Binding of the Src SH2 domain to phosphopeptides is determined by residues in both the SH2 domain and the phosphopeptides. (1993)

Src homology 2 (SH2) domains are found in a variety of signaling proteins and bind phosphotyrosine-containing peptide sequences. To explore the binding properties of the SH2 domain of the Src protein kinase, we used immobilized phosphopeptides to bind purified glutathione S-transferase-Src SH2 fusion proteins. With this assay, as well as a free-peptide competition assay, we have estimated the affinities of the Src SH2 domain for various phosphopeptides relative to a Src SH2-phosphopeptide interaction whose Kd has been determined previously (YEEI-P; Kd = 4 nM). Two Src-derived phosphopeptides, one containing the regulatory C-terminal Tyr-527 and another containing the autophosphorylation site Tyr-416, bind the Src SH2 domain in a specific though low-affinity manner (with about 10(4)-lower affinity than the YEEI-P peptide). A platelet-derived growth factor receptor (PDGF-R) phosphopeptide containing Tyr-857 does not bind appreciably to the Src SH2 domain, suggesting it is not the PDGF-R binding site for Src as previously reported. However, another PDGF-R-derived phosphopeptide containing Tyr-751 does bind the Src SH2 domain (with an affinity approximately 2 orders of magnitude lower than that of YEEI-P). All of the phosphopeptides which bind to the Src SH2 domain contain a glutamic acid at position -3 or -4 with respect to phosphotyrosine; changing this residue to alanine greatly diminishes binding. We have also tested Src SH2 mutants for their binding properties and have interpreted our results in light of the recent crystal structure solution for the Src SH2 domain. Mutations in various conserved and nonconserved residues (R155A, R155K, N198E, H201R, and H201L) cause slight reductions in binding, while two mutations cause severe reductions. The W148E mutant domain, which alters the invariant tryptophan that marks the N-terminal border of the SH2 domain, binds poorly to phosphopeptides. Inclusion of the SH3 domain in the fusion protein partially restores the binding by the W148E mutant. A change in the invariant arginine that coordinates twice with phosphotyrosine in the peptide (R175L) results in a nearly complete loss of binding. The R175L mutant does display high affinity for the PDGF-R peptide containing Tyr-751, via an interaction that is at least partly phosphotyrosine independent. We have used this interaction to show that the R175L mutation also disrupts the intramolecular interaction between the Src SH2 domain and the phosphorylated C terminus within the context of the entire Src protein; thus, the binding properties observed for mutant domains in an in vitro assay appear to mimic those that occur in vivo.
Microbiological study of transtracheal aspirates from dogs with suspected lower respiratory tract disease: 264 cases (1989-1995) (1997)

Amikacin, ceftizoxime, enrofloxacin, and gentamicin may be rational choices for treatment of suspected infectious lower respiratory tract disease of dogs, before identification of the causative agent(s) and before results of susceptibility tests become available.
QTL analysis of transgressive segregation in an interspecific tomato cross. (1993)

Two accessions, representing the species Lycopersicon esculentum (cultivated tomato) and Lycopersicon pennellii (a wild relative), were evaluated for 11 quantitative traits and found to be significantly different for 10 of the traits. Transgressive segregation was observed for eight of the traits in a large interspecific F2 population. When restriction fragment length polymorphism markers were used as probes for the quantitative trait loci (QTL) underlying the traits, 74 significant QTL (LOD > 2) were detected. Thirty-six percent of those QTL had alleles with effects opposite to those predicted by the parental phenotypes. These QTL were directly related to the appearance of transgressive individuals in the F2 for those traits which showed transgressive segregation. However, the same types of QTL (with allelic effects opposite to those predicted by the parents) were also observed for traits that did not display transgressive segregation in the F2. One such trait was dry weight accumulation. When two overdominant QTL (detected in the F2) for this trait were backcrossed into the L. esculentum genetic background, transgressive individuals were recovered and their occurrence was associated with the two QTL demonstrating the potential for transgressive segregation for all characters and implicating overdominance as a second cause of transgressive segregation. Epistasis was not implicated in transgressive segregation in either the F2 or backcross generations. Results from this research not only reveal the basis of wide-cross transgressive segregation, but demonstrate that molecular markers can be used to identify QTL (from wild species) responsible for transgressive phenotypes and to selectively transfer them into crop species. This strategy might be used to improve many traits of economic importance including those for which wild species appear phenotypically inferior to their cultivated counterparts.
Siglecs Facilitate HIV-1 Infection of Macrophages through Adhesion with Viral Sialic Acids (2011)

Our study showed that sialic acids on the viral envelope facilitated HIV-1 infection of macrophages through interacting with Siglec receptors, and the expression of Siglec-1 correlated with viral sialic acid-mediated host attachment. This glycan-mediated viral adhesion underscores the importance of viral sialic acids in HIV infection and pathogenesis, and suggests a novel class of antiviral compounds targeting Siglec receptors.
Electrical Control of Individual Droplet Breaking and Droplet Contents Extraction (2011)

The controllable extraction of the contents from an individual droplet is very important for the analysis and further processing of droplets. Most of the available methods lack the control and flexibility over the extraction of droplet contents. Here, we present a novel electrical-based method that can selectively break a droplet and extract its contents into aqueous buffer in a controllable manner on a microfluidic device. The device consisted of two layers, in which the top layer was modified to be hydrophobic for droplet generation and the bottom layer modified to be hydrophilic for maintaining aqueous buffer. A stable oil/water interface was formed at the intersection of the two layers where the oil and aqueous buffer met. When a droplet flew through the oil/water interface, a voltage was applied in the aqueous buffer. The generated electro-osmotic flow in the aqueous buffer and the electric field facilitated the breaking of the water/oil interface between the droplet and aqueous buffer, promoting the breaking of the droplet and a transient coalescence of the droplet with aqueous buffer. During the transient coalescence, droplet contents could be extracted into aqueous buffer. The amount of the droplet contents extracted into the aqueous buffer could be controlled by varying the strength of the electric field, and the droplet still existed and could be further processed after complete extraction of the droplet contents. This method could be used for droplet analysis and may provide a way to perform complex fluid handling in a droplet.
Assessment of iron stores in children with transfusion siderosis by biomagnetic liver susceptometry (1999)

To investigate the applicability of noninvasive Superconducting Quantum Interference Device (SQUID) biomagnetic liver susceptometry and its limitations in thalassemic children, 23 patients with beta-thalassemia major and other iron loading anemias (age: 4-16 years) and 16 age-related normal children were studied. Liver iron concentrations ranged from 600 to 11,000 microg/g(liver) for thalassemic patients and from 60 to 340 microg/g(liver) for normal patients. Measuring the respective organ volumes by sonography, liver and spleen iron stores, accounting for 80% of total body iron stores, were estimated. Nonliver contributions from the lung or intestine to the measured SQUID signals in the small-sized patients were not observed. Moreover, livers in thalassemia were found to be enlarged by 18% per 1,000 microg/g (r = 0.75, P < 10(-3)). Serum ferritin values correlate significantly with iron stores (r = 0.64, P < 10(-3)), but predict iron stores only within large error intervals of 4,000 microg/g(liver). Analyzing the experimental data from biomagnetometry and from related transfusion and chelation treatment data within the framework of a two-compartment model, we were able to derive additional information on total body iron elimination and chelation therapy efficacy. The exponential decline of iron stores allows forecast of steady-state conditions of the final iron load for a particular transfusion and chelation therapy regimen.
Therapeutic Approaches to Osteoarthritis (1997)

Management is multifaceted: Palliation of pain should be accompanied by physical and occupational therapy and use of adaptive devices to improve performance. New techniques aim to interrupt disease progression and to induce biologic repair.
Slowed Release of Thrombin-cleaved Factor VIII from von Willebrand Factor by a Monoclonal and a Human Antibody Is a Novel Mechanism for Factor VIII Inhibition (1996)

The anti-factor VIII (fVIII) C2 domain monoclonal antibody ESH8 inhibits fVIII activity only when fVIII is bound to von Willebrand factor (vWf). However, ESH8 binds with similar affinity to fVIII and fVIII.vWf complex, and it does not affect the kinetics of thrombin cleavage at positions 372 and 740 within the fVIII heavy chain and at 1689 within the light chain. The latter is required for fVIII release from vWf. We showed that ESH8 reduced the initial rate of thrombin-activated fVIII (fVIIIa) release from vWf by 4.3-fold compared to that in the absence of antibody. The complex of vWf. fVIII.ESH8 was activated, and the rate constant determined for fVIIIa dissociation from vWf was 4 x 10(-3) s-1. We constructed a mathematical model incorporating the measured rates for fVIIIa release from vWf and for inactivation of heterotrimeric fVIIIa due to the spontaneous loss of the A2 subunit and found that the decreased release rate is sufficient to explain our experimentally observed inhibition of fVIII activity by ESH8. We hypothesize that the slowed rate of fVIIIa release from vWf in the presence of ESH8 allows time for inactivation of unstable fVIIIa prior its participation in the formation of the factor Xase complex. The relevance of these findings is illustrated by our observation that reduction of fVIIIa release from vWf represents an additional mechanism of fVIII inhibition by an anti-C2 domain antibody (epitope 2218-2307) from a hemophilia A patient. This rare antibody binds to a more amino-terminal epitope than other human anti-C2 inhibitors, resulting in its lack of inhibition of fVIII binding to vWf but not to phospholipid. These two fVIII ligands therefore bind to C2 sites which do not overlap completely.
In Vivo and In Vitro Intragenomic Rearrangement of TT Viruses (2007)

The in vitro replication of the Torque teno virus (TT virus) tth8 full-length genome and particle formation in a Hodgkin's lymphoma-derived cell line after transfection with cloned viral DNA were demonstrated. Analyses of the transcription patterns of tth8 and tth7 TT virus isolates in a number of lymphoma and T-cell leukemia cell lines indicated differential additional splicing events and intragenomic rearrangement generating open reading frames which could not be deducted from the genomic sequence. We also demonstrated the presence of rearranged TT virus genomes in vivo in sera taken from pregnant mothers whose children later developed childhood leukemia, as well as sera from control mothers. Control experiments using religated cloned genomic tth8 DNA mixed with cellular DNA did not result in such subviral molecules. These subviral isolates ranged from 172 bp to full-length TT virus genomes. Possible in vivo selection for specific rearranged molecules was indicated by the presence of one isolate (561 bp) in 11 serum samples. It remains to be clarified whether selected rearranged subviral components resulting from specific TT virus types may contribute to the initiation of disease. These data demonstrate new features of TT viruses suggesting possible similarities to plant viruses of the family Geminiviridae, as well as raise questions about the documented plurality and diversity of anelloviruses.
High urea and NaCl carbonylate proteins in renal cells in culture andin vivo, and high urea causes 8-oxoguanine lesions in their DNA (2004)

(i) Oxidative stress, associated with high urea, causes 8-oxoguanine DNA lesions in mIMCD3 cell DNA. (ii) High urea or NaCl carbonylates proteins in mIMCD3 cells and in renal inner medullary cells in vivo. (iii) In mIMCD3 cells a normal plasma concentration of urea causes carbonylation, and carbonylation increases over the uremic range of urea concentration, indicating that urea can contribute directly to the carbonylation found in uremia.
The link‐prediction problem for social networks (2007)

Abstract Given a snapshot of a social network, can we infer which new interactions among its members are likely to occur in the near future? We formalize this question as the link‐prediction problem , and we develop approaches to link prediction based on measures for analyzing the “proximity” of nodes in a network. Experiments on large coauthorship networks suggest that information about future interactions can be extracted from network topology alone, and that fairly subtle measures for detecting node proximity can outperform more direct measures.
Treosulfan induces distinctive gonadal toxicity compared with busulfan (2018)

Treosulfan (L-treitol-1,4-bis-methanesulfonate) has been increasingly incorporated as a main conditioning protocol for hematopoietic stem cell transplantation in pediatric malignant and non-malignant diseases. Treosulfan presents lower toxicity profile than other conventional alkylating agents containing myeloablative and immunosuppressive traits such as busulfan. Yet, whereas busulfan is considered highly gonadotoxic, the gonadal toxicity profile of treosulfan remains to be elucidated. To study the gonadotoxicity of treosulfan, pubertal and prepubertal male and female mice were injected with treosulfan or busulfan and sacrificed one week, one month or six months later. Testicular function was assessed by measurements of sperm properties, testes and epididymides weights as well as markers for testicular reserve, proliferation and apoptosis. Ovarian function was assessed by measurements of ovary weight and markers for ovarian reserve, proliferation and apoptosis. Treosulfan testicular toxicity was milder than that of busulfan toxicity; possibly by sparing the stem spermatogonia in the testicular sanctuary. By contrast, ovarian toxicity of both treosulfan and busulfan was severe and permanent and displayed irreversible reduction of reserve primordial follicles in the ovaries. Our data indicate that treosulfan exerts a different gonadal toxicity profile from busulfan, manifested by mild testicular toxicity and severe ovarian toxicity.
Alteration of chain length selectivity of aRhizopus delemar lipase through site‐directed mutagenesis (1994)

The coding sequences of the Rhizopus delemar lipase and prolipase were altered by oligonucleotide-directed mutagenesis to introduce amino acid substitutions. The resulting mutant enzymes, synthesized by the bacterial host Escherichia coli BL21 (DE3), were tested for their ability to hydrolyze the triglycerides triolein (TO), tricaprylin (TC) and tributyrin (TB). Mutagenesis and lipase gene expression were carried out using plasmid vectors derived from previously described recombinant plasmids [Joerger and Haas (1993) Lipids 28, 81-88] by introduction of the origin of replication of bacteriophage f1. Substitution of threonine 83 (thr83), a residue thought to be involved in oxyanion binding, by alanine essentially eliminated lipolytic activity toward all substrates examined (TB, TO and TC). Replacement of thr83 with serine caused from two- to sevenfold reductions in the activity toward these substrates. Introduction of tryptophan (trp) at position 89, where such a residue is found in closely related fungal lipases, reduced the specific activity toward the three triglyceride substrates. For the mutagenesis of residues in the predicted acyl chain binding groove, mutagenic primers were designed to cause the replacement of a specific codon within the prolipase gene with codons for all other amino acids. Phenylalanine 95 (phe95), phe112, valine 206 (val206) and val209, were targeted. A phenotypic screen was successfully employed to identify cells producing prolipase with altered preference for olive oil, TC or TB. In assays involving equimolar mixtures of the three triglycerides, a prolipase with a phe95-->aspartate mutation showed an almost twofold increase in the relative activity toward TC. Substitution of trp for phe112 caused an almost threefold decrease in the relative preference for TC, but elevated relative TB hydrolysis. Replacement of val209 with trp resulted in an enzyme with a two- and fourfold enhanced preference for TC and TB, respectively.
Removal of heparin and protamine from plasma. (1976)

A simple chromatographic technique for rapid adsorption of heparin and protamine from plasma samples is described, allowing accurate interpretation of coagulation screening tests and specific clotting factor assays. With the use of columns of ECTEOLA-cellulose, up to 300 U. of heparin could be completely adsorbed from a 1 ml. plasma sample. When citrated nonheparinized plasma was passed over the ECTEOLA-cellulose columns, the thrombin, prothrombin, and partial thromboplastin times were unaffected. Levels of fibrinogen, prothrombin, and factors V, VII, VIII, IX, and XI average within 90 per cent of control, nonchromatographed samples. When heparinized plasma samples (0.1 and 1.0 U. per milliliter) were passed over columns, heparin was completely removed and the results of the screening tests and the specific factor assays were the same as for the chromatographed nonheparinized samples. In addition, heparinized samples with decreased factor VIII activity maintained their pretreatment factor VII activities after heparin removal. Blood samples containing heparin were obtained from two patients during open-heart surgery. Following heparin adsorption on ECTEOLA-cellulose columns, factor VIII activity levels remained above 60 per cent during cardiopulmonary by-pass. The presence of protamine sulfate in plasma samples prolonged the prothrombin and partial thromboplastin times while slightly shortening the thrombin time. The protamine effect persisted after ECTEOLA-cellulose, but could be removed by a similar column of carboxymethyl-cellulose. The latter resin had no effect on screening tests or on assays of factors VIII or IX activity. The combination of the two resins was then used to remove the separate inhibitory effects from heparinized plasma samples to which protamine had been added.
Navigating hierarchically clustered networks through fisheye and full-zoom methods (1996)

Many information structures are represented as two-dimensional networks (connected graphs) of links and nodes. Because these network tend to be large and quite complex, people often perfer to view part or all of the network at varying levels of detail. Hierarchical clustering provides a framework for viewing the network at different levels of detail by superimposing a hierarchy on it. Nodes are grouped into clusters, and clusters are themselves place into other clusters. Users can then navigate these clusters until an appropiate level of detail is reached. This article describes an experiment comparing two methods for viewing hierarchically clustered networks. Traditional full-zoom techniques provide details of only the current level of the hierarchy. In contrast, fisheye views, generated by the “variable-zoom” algorithm described in this article, provide information about higher levels as well. Subjects using both viewing methods were given problem-solving tasks requiring them to navigate a network, in this case, a simulated telephone system, and to reroute links in it. Results suggest that the greater context provided by fisheye views significantly improved user performance. Users were quicker to complete their task and made fewer unnecessary navigational steps through the hierarchy. This validation of fisheye views in important for designers of interfaces to complicated monitoring systems, such as control rooms for supervisory control and data acquistion systems, where efficient human performance is often critical. However, control room operators remained concerned about the size and visibility tradeoffs between the fine room operators remained concerned about the size and visibility tradeoffs between the fine detail provided by full-zoom techniques and the global context supplied by fisheye views. Specific interface feaures are required to reconcile the differences.
Embodiment and Luminescence Properties of Sr<sub>3</sub>SiO<sub>5</sub>:Eu(Yellow-Orange Phosphor) by Co-Doping Lanthanide (2007)

We have synthesized a Eu2+-activated lanthanide co-doped Sr3SiO5 : Eu yellow-orange phosphor. In this experiment, sample powder has been synthesized by conventional solid state method. It was calculated that luminescent efficiency of a Gd3+ co-doped Sr3SiO5:Eu phosphor sample is up to 105% than that of only Sr3SiO5:Eu phosphor. Those samples can be applied such as phosphor for white LED lamps through integrating on the UV or blue chips. On the contrary, the use of a Dy, Ce, Pr and lanthanide short of Gd by the co-doping materials was caused by decreasing luminescent intensity. The emission band was shifted from 572nm to short wavelengths by co-doping lanthanide. The emission band of a Nd3+ co-doped Sr3SiO5 : Eu phosphor sample was not symmetrical at 570nm. As Nd3+ concentration increased, two emission bands were observed
Problems in Adapting a Glucose-Oxidase Electrochemical Sensor into an Implantable Glucose-Sensing Device (1982)

International audience