gebhart/patrepeval huggingface dataset:
Development and Qualification of an Opsonophagocytic Killing Assay To Assess Immunogenicity of a Bioconjugated Escherichia coli Vaccine (2017)

The global burden of disease caused by extraintestinal pathogenic <i>Escherichia coli</i> (ExPEC) is increasing as the prevalence of multidrug-resistant strains rises. A multivalent ExPEC O-antigen bioconjugate vaccine could have a substantial impact in preventing bacteremia and urinary tract infections. Development of an ExPEC vaccine requires a readout to assess the functionality of antibodies. We developed an opsonophagocytic killing assay (OPA) for four ExPEC serotypes (serotypes O1A, O2, O6A, and O25B) based on methods established for pneumococcal conjugate vaccines. The performance of the assay was assessed with human serum by computing the precision, linearity, trueness, total error, working range, and specificity. Serotypes O1A and O6A met the acceptance criteria for precision (coefficient of variation for repeatability and intermediate precision, ≤50%), linearity (90% confidence interval of the slope of each strain, 0.80, 1.25), trueness (relative bias range, -30% to 30%), and total error (total error range, -65% to 183%) at five serum concentrations and serotypes O2 and O25B met the acceptance criteria at four concentrations (the lowest concentration for serotypes O2 and O25B did not meet the system suitability test of maximum killing of ≥85% of <i>E. coli</i> cells). All serotypes met the acceptance criteria for specificity (opsonization index value reductions of ≤20% for heterologous serum preadsorption and ≥70% for homologous serum preadsorption). The assay working range was defined on the basis of the lowest and highest concentrations at which the assay jointly fulfilled the target acceptance criteria for linearity, precision, and accuracy. An OPA suitable for multiple <i>E. coli</i> serotypes has been developed, qualified, and used to assess the immunogenicity of a 4-valent <i>E. coli</i> bioconjugate vaccine (ExPEC4V) administered to humans.
Application of a Rotor–Stator High-Shear System for Cr/Mn-Mediated Reactions in Eribulin Mesylate Synthesis (2015)

Potential issues associated with the scale up of a catalytic Nozaki–Hiyama–Kishi reaction and a Cr/Mn-mediated desulfonylation used in eribulin mesylate synthesis were evaluated, and countermeasures were investigated. When stir bar agitation, which is typically used for laboratory-scale reactions, was changed to impeller-type agitation upon scale up of these reactions, the conversion rate and yield decreased considerably. Traditional methods for overcoming such decreases, such as preactivation of the Mn or the use of fine particles of Mn, did not improve the conversion rate sufficiently, whereas a physical shearing approach was effective. Specifically, we found that the use of a rotor–stator high-shear system as a stirring device afforded the same conversion rate as that observed with a stir bar.
Dinámica de la composición de especies en bosques de Quercus crassipes H. et B. en Cerro Grande, Sierra de Manantlán, México (2000)

With the purpose to know about the dynamics of species composition in forests dominated by oaks (Quercus spp.), and its implications for forest management,...
Investigating the microstructure of a yield-stress fluid by light scattering (2011)

We report the results of an experimental study of the microstructure of dispersions of Carbopol ETD 2050, a model yield-stress fluid. Using two different light scattering instruments, measurements were made over three decades in scattering wave vector, from 0.02 to 25 μm⁻¹. These measurements reveal microstructure characterized by two length scales: a longer length scale, 6 μm and larger, that depends on Carbopol concentration and the pH of the dispersion and a shorter length scale of approximately 400 nm that is independent of both sample concentration and pH. We relate these results to shear rheology measurement of the yield stress of these materials.
THE EFFECTS OF DEFECTS ON MELTING OF COPPER (2009)

With molecular dynamics (MD) simulations, we investigate the effects of defects on Cu melting under ambient pressure and shock wave loading. We explore preexistent defects including vacancies, stacking faults and grain boundaries, as well as shock‐induced defects. Depending on defect characteristics (energy and concentration), defects may have negligible or considerable effects on melting at MD time and length scales. It is expected that defects have more pronounced effects at heating rates lower than the MD rates.
An Ultraviolet-Curable Mold for Sub-100-nm Lithography (2004)

We describe a novel UV-curable mold that is stiff enough for replicating dense sub-100-nm features even with a high aspect ratio. It also allows for flexibility when the mold is prepared on a flexible support such that large area replication can be accomplished. The composite material of the mold is inert to chemicals and solvents. The surface energy is made low with a small amount of releasing agent such that the mold can be removed easily and cleanly after patterning. In addition, the material allows self-replication of the mold. These unique features of the mold material should make the mold quite useful for various patterning purposes.
Poly(amido-amine)s: Biomedical Applications (2002)

Poly(amido-amine)s (PAAs) are synthetic tert-amino polymers obtained by stepwise polyaddition of primary or secondary aliphatic amines to bis(acrylamide)s. Linear polymers are produced during the polymerisation of both primary mono(amine)s and secondary bis(amine)s. Under non-selective conditions primary bis(amine)s usually give crosslinked products upon reaction with bis(acrylamide)s, i. e., they react as tetrafunctional monomers. Furthermore, end-functionalised PAAs can be used to prepare block or graft copolymers, as well as crosslinked resins. PAAs can therefore be regarded as macromonomers as well. Generally, PAAs are soluble in water, chloroform, lower alcohols, dimethyl sulfoxide and other polar solvents (although amphoteric PAAs can only be dissolved in water). PAAs are degradable in aqueous solution by means of hydrolytic cleavage of the amidic bonds in their main chain that are activated by the tert-amino groups present in ?-position. A vast library of PAA structures has now been reported that are suitable for numerous material and biomedical applications. Here we review the synthesis, characterisation and current biomedical uses of PAAs. Their use as heavy-metal-ion-complexing polymers, and polymers for heparin neutralisation in solution, fabrication of heparin-absorbing resins and heparinisable materials is discussed. As amphoteric PAAs are biocompatible and biodegradable polymers that moreover display intelligent stealth properties, they are currently under development as PAA/anticancer conjugates and non-viral vectors for intracytoplasmic delivery. The potential of this unique chemistry is reviewed.
Design and Analysis of a Droop Nose for Coanda Flap Applications (2014)

The present study describes the fundamentals of droop nose design for improving the aerodynamics of airfoils with active high-lift using an internally blown Coanda-type flap. The main objectives are to increase the stall angle of attack and reduce the power required by the high-lift system. A two-dimensional sensitivity analysis explores the effects of varying airfoil camber and thickness in the first 20% of the chord. The resulting droop nose configuration improves the maximum lift coefficient by about 20% and increases the stall angle of attack by around 10–15 deg. A target lift coefficient of about 4.7 is reached with 28% less jet momentum coefficient, compared to the clean nose. As the modified leading-edge geometry presents different stall mechanisms, the aerodynamic response to variations of jet momentum is also different. In particular, for a jet momentum coefficient above 0.035, the stall angle of attack increases with jet momentum, in contrast with the behavior observed with the clean nose.
Enzymatic degradation of uracil-containing deoxyribonucleic acid. V. Survival of Escherichia coli and coliphages treated with sodium bisulfite (1979)

A number of mutants of Escherichia coli defective in the ung gene (structural gene for uracil-deoxyribonucleic acid [ura-DNA] glycosylase) are shown to be abnormally sensitive to treatment with sodium bisulfite when compared with congenic ung+ strains. These results provide further evidence that sodium bisulfite causes the deamination of cytosine to uracil in DNA and that ura-DNA glycosylase is required for the repair of U-G mispairs. The effect of the chemical is apparently selective with respect to base damage; coliphages containing cytosine in their DNA are inactivated by treatment with sodium bisulfite, whereas those containing hydroxymethylcytosine are not. ura-DNA glycosylase and the major apurinic-apyrimidinic endonuclease of E. coli may function in the same repair pathway, since the extent of inactivation of a congenic set of strains which are ung xth (structural gene for the major apurinic-apyrimidinic endonuclease of E. coli) or ung xth+ is the same.
Monitoring gastric cancer progression with circulating tumour DNA (2014)

ctDNA may serve as a useful biomarker to monitor gastric cancer progression and residual disease.
Effects of the bactericidal/permeability-increasing protein of polymorphonuclear leukocytes on isolated bacterial cytoplasmic membrane vesicles (1988)

The bactericidal/permeability-increasing protein (BPI) of polymorphonuclear leukocytes is a potent bactericidal agent specific for gram-negative bacteria. The protein blocks bacterial multiplication without substantially inhibiting the uptake and incorporation of macromolecular precursors, suggesting that the cytoplasmic membrane escapes early injury. Because greater than 90% of bound BPI can be removed from the bacterial surface sites after irreversible loss of viability, it was uncertain whether BPI reaches the cytoplasmic membrane and, if so, affects its functions. This study shows that BPI caused similar dose-dependent inhibition of O2 consumption and metabolic energy-dependent amino acid transport by cytoplasmic membrane vesicles of both gram-negative (Escherichia coli) and gram-positive (Bacillus subtilis) bacteria. Near maximal inhibition occurred at BPI doses that caused complete killing of an equivalent number of intact E. coli, with binding of BPI to membrane vesicles that was less than or equal to 10% of binding to intact (BPI-sensitive) bacteria. The effects of BPI and of the membrane-disruptive peptide antibiotic polymyxin B on membrane vesicles were distinctly different, indicating that the two agents affect membrane function by different mechanisms. BPI also rapidly inhibited O2 consumption by intact E. coli, with minimal impairment of bacterial protein synthesis. Thus, BPI is capable of damaging the cytoplasmic membrane of both gram-negative and gram-positive bacteria and of inhibiting at least one cytoplasmic membrane-associated function in intact E. coli. The relationship between these effects and the mechanism of bacterial killing by BPI remains to be established.
Evaluation of antioxidant properties of marine microalga Chlorella marina (Butcher, 1952) (2012)

To evaluate the in vitro antioxidant capacity of a Chlorella marina (Butcher, 1952). Samples were tested for the total phenolic content, antioxidant activity, deoxy ribose radical scavenging activity and reducing power. The methanolic extract was found to have high levels of phenolic (0.647±0.052 mg GAE/g), when compared to diethyl ether and hexane. The diethyl ether extract exhibited higher antioxidant potential as (0.816±0.366 mg AscAE/ g), higher percentage of deoxy ribose radical scavenging activity (0.399±0.004) and reducing power (2.814±0.014). The phenolic compounds were not a major contributor to the antioxidant capacities of these microalgae. This was very different from many other plant species like fruits, vegetables and medicinal plants. The microalgae could contain different antioxidant compounds from other plants.
New Options in Noninvasive Assessment of Left Ventricular Torsion (2008)

The complex, intricate 3D pattern of ventricular torsion has both fascinated and perplexed scientists for centuries. The identity of the underlying anatomic myocardial unit responsible for this pattern of contraction continues to be an arena of debate. While the complicated wringing motions involved in torsion are difficult to quantify, several techniques have been demonstrated to be effective in the noninvasive assessment of left ventricular (LV) torsion. Magnetic resonance tissue-tagging with dynamic MRI is the gold standard for the noninvasive quantitative evaluation of torsion with high spatial and temporal resolution. However, this is a technically involved and potentially time-consuming process. Echocardiography is another alternative noninvasive method. Both tissue Doppler imaging and speckle-tracking imaging have been shown to be sufficiently accurate and reliable alternatives to MRI in the noninvasive assessment of LV torsion. While the potential applications of these techniques to assess LV torsion appears boundless, further studies are needed to validate measures of LV torsion by the additional, but most important, test of demonstrating its clinical utility as a predictor of prognosis.
Riboflavin-Sensitized Photoöxidation of Indoleacetic Acid and Related Compounds (1949)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Ability of lactoferrin to promote the growth of Bifidobacterium spp. in vitro is independent of receptor binding capacity and iron saturation level (1999)

Lactoferrin (Lf) is an iron-binding protein which has been shown to inhibit the growth of various bacterial pathogens and promote the growth of anaerobic bacteria of the genus Bifidobacterium in vitro. The present study was designed to investigate whether the bifidobacteria growth promotion activity of Lf is correlated with either the binding of Lf to bifidobacterial cells or the iron saturation of Lf. Bovine Lf (bLf) from mature milk increased the growth of B. infantis and B. breve in vitro in a dose-dependent fashion, while much less growth promotion activity was found for B. bifidum. In contrast, human Lf (huLf) from mature milk promoted the growth of B. bifidum and was inactive for B. infantis and B. breve, while bLf from colostrum was devoid of bifidobacteria growth promotion activity. Changes in the iron content of Lf did not alter the bifidobacteria growth promotion activity of either bLf or huLf preparations. Competitive binding studies with biotinylated milk bLf showed that binding of bLf was inhibited by unlabelled bLf and huLf but not by beta-lactoglobulin, alpha-lactalbumin or transferrin. Binding of bLf to B. bifidum and B. breve was c. 40-fold higher than binding to Escherichia coli. Colostrum bLf was also found to bind to B. bifidum and B. breve, despite a lack of in-vitro growth promotion activity. Collectively, these results demonstrate that the ability of Lf to promote the growth of Bifidobacterium spp. in vitro is independent of the iron saturation level for Lf and suggest that binding of Lf to bifidobacteria cells may be involved but is not sufficient for stimulation of bifidobacterial growth.
A Readily Synthesized and Highly Active Epoxide Carbonylation Catalyst Based on a Chromium Porphyrin Framework:  Expanding the Range of Available β-Lactones (2004)

Catalytic carbonylation of epoxides to β-lactones was effected by a highly active and selective bimetallic catalyst comprised of a chromium(III) porphyrin cation and a cobalt tetracarbonyl anion. The complex is readily synthesized from commercially available compounds in high yield. Carbonylation of numerous linear epoxides, as well as bicyclic epoxides derived from 8- and 12-membered hydrocarbons, proceeded with high activity, selectivity, and yield.
Investigation of periodically poled lithium niobate crystals by light diffraction (2005)

Periodically poled lithium niobate crystals are investigated by illumination along the crystallographic c axis while applying an external electric field. The resulting diffraction patterns are in good agreement with the results of numerical simulations and directly yield first information such as periodicity, duty cycle, and homogeneity of the domain patterns.
Experimental approaches to evaluate endothelin-A receptorantagonists (2004)

A large body of evidence suggests a substantial role of the endothelin (ET) system in the pathophysiology of a variety of disease states, mainly of the cardiovascular system. Recently bosentan, an ET receptor antagonist, has received approval by the Food and Drug Administration (FDA) for use in pulmonary artery hypertension. The ET system may also be involved in cerebrovascular disorders such as stroke and, most notably, development of cerebral vasospasm following subarachnoid hemorrhage. The pathophysiological mechanisms contributing to the development of a cerebral vasospasm after subarachnoid hemorrhage may be taken as a paradigm to explore mechanisms leading to secondary ischemic brain damages in a variety of insults such as stroke and trauma. The present review provides the evidence to evaluate ET receptor antagonists for potential prophylactic and therapeutic use in patients suffering from subarachnoid hemorrhage. The rationale to develop selective ETA receptor antagonists is given with respect to basic and applied studies. This may be useful to better define the desired profile of action of a given compound, and it may also help to design appropriate preclinical and clinical trials, most desirably in close cooperation with pharmaceutical companies and neurosurgical departments.
Functional Participation of the IL-2 Receptor γ Chain in IL-7 Receptor Complexes (1994)

The gamma chain of the interleukin-2 (IL-2) receptor is shared with the functional IL-4 receptor and is causatively related to X-linked severe combined immunodeficiency (XSCID), which is ascribed to a profound T cell defect. Studies with monoclonal antibodies specific for the IL-2 receptor gamma chain showed that the gamma chain participates in the functional high-affinity receptor complexes for IL-7 that are involved in the differentiation of T and B cells. Participation of the gamma subunit in more than one receptor may enable the elucidation of the mechanisms of XSCID development and lymphocyte differentiation.
Partial inactivation of the RB product in a family with incomplete penetrance of familial retinoblastoma and benign retinal tumors. (1994)

While familial retinoblastoma has served as the paradigm for the two-hit theory of tumorigenesis and for the concept of the tumor suppressor gene, the etiology of incomplete penetrance of familial retinoblastoma is poorly understood. To address the molecular basis for this phenotype we have studied the functional properties of a mutant Rb gene identified in a kindred with incomplete penetrance of familial retinoblastoma and evidence for regressed retinal lesions (retinomas). In contrast to all previously isolated RB mutant proteins, we demonstrated that the mutant product from this kindred retained the wildtype properties of nuclear localization, the ability to undergo hyperphosphorylation in vivo, and the capacity to suppress growth of RB(-) cells. Protein binding ('pocket') activity, however, was defective defining a new class of RB mutant with partial inactivation. The presence of this unique RB mutant in the germline of obligate carriers with incomplete penetrance and regressed retinal lesions suggests a molecular basis for this phenotype and supports the hypothesis that a minimum 'RB threshold' level of protein binding activity is required to suppress tumorigenesis.
Manipulating particle trajectories with phase-control in surface acoustic wave microfluidics (2011)

We present a 91 MHz surface acoustic wave resonator with integrated microfluidics that includes a flow focus, an expansion region, and a binning region in order to manipulate particle trajectories. We demonstrate the ability to change the position of the acoustic nodes by varying the electronic phase of one of the transducers relative to the other in a pseudo-static manner. The measurements were performed at room temperature with 3 μm diameter latex beads dispersed in a water-based solution. We demonstrate the dependence of nodal position on pseudo-static phase and show simultaneous control of 9 bead streams with spatial control of -0.058 μm/deg ± 0.001 μm/deg. As a consequence of changing the position of bead streams perpendicular to their flow direction, we also show that the integrated acoustic-microfluidic device can be used to change the trajectory of a bead stream towards a selected bin with an angular control of 0.008 deg/deg ± 0.000(2) deg/deg.
Equine Herpesvirus-2 E10 Gene Product, but Not Its Cellular Homologue, Activates NF-κB Transcription Factor and c-Jun N-terminal Kinase (1999)

We have previously reported on the death effector domain containing E8 gene product from equine herpesvirus-2, designated FLICE inhibitory protein (v-FLIP), and on its cellular homologue, c-FLIP, which inhibit the activation of caspase-8 by death receptors. Here we report on the structure and function of the E10 gene product of equine herpesvirus-2, designated v-CARMEN, and on its cellular homologue, c-CARMEN, which contain a caspase-recruiting domain (CARD) motif. c-CARMEN is highly homologous to the viral protein in its N-terminal CARD motif but differs in its C-terminal extension. v-CARMEN and c-CARMEN interact directly in a CARD-dependent manner yet reveal different binding specificities toward members of the tumor necrosis factor receptor-associated factor (TRAF) family. v-CARMEN binds to TRAF6 and weakly to TRAF3 and, upon overexpression, potently induces the c-Jun N-terminal kinase (JNK), p38, and nuclear factor (NF)-kappaB transcriptional pathways. c-CARMEN or truncated versions thereof do not appear to induce JNK and NF-kappaB activation by themselves, nor do they affect the JNK and NF-kappaB activating potential of v-CARMEN. Thus, in contrast to the cellular homologue, v-CARMEN may have additional properties in its unique C terminus that allow for an autonomous activator effect on NF-kappaB and JNK. Through activation of NF-kappaB, v-CARMEN may regulate the expression of the cellular and viral genes important for viral replication.