gebhart/patrepeval huggingface dataset:
Protective effects of hydroxyethyl starch-deferoxamine in early sepsis. (1995)

The protective effects of hydroxyethyl starch-conjugated deferoxamine (HES-DFO), a macromolecular iron chelator, on the initial pathophysiological cascade in septic shock were evaluated following cecal ligation puncture (CLP) in rats. Animals were given an intravenous dose of 3.0 mL of either vehicle (HES) or HES-DFO immediately following completion of the CLP procedure. Animals were sacrificed 30, 60, 120, and 240 min following CLP, and samples of lung, kidney, bowel, and liver were collected for subsequent analysis of glutathione, myeloperoxidase, and evidence for lipid peroxidation based on measurement of thiobarbituric acid reactive substances and conjugated dienes. In addition, the endotoxin levels were determined in the plasma and histomorphological examination was conducted on tissue samples collected at each time point. At almost all time points, a reduction in lipid peroxidation was noted in the HES-DFO-treated rats (p < .05). Glutathione and myoloperoxidase levels were less affected. Lung tissue from animals receiving HEs demonstrated marked microatelectases, septal destruction, and splicing of basal membranes, which were greatly attenuated in animals having received HES-DFO. Similarly, tubulotoxic and mitochondrial damages observed in kidney samples from HES-treated animals were noticeably reduced in the animals having received the chelator. Liver and gut samples demonstrated unspecific inflammatory injury in both groups of animals. In summary, oxygen radical-mediated tissue damage occurs rapidly following CLP-induced sepsis. Based on histological and biochemical endpoints, treatment with the polymeric iron chelator, HES-DFO, significantly attenuates systemic oxidant injury, the degree of protection being most impressive in the lung and kidney.
<title>Recent developments in the application of optical frequency domain reflectometry to distributed Bragg grating sensing</title> (2002)

This paper presents recent developments in the use of optical frequency domain reflectometry (OFDR) to measure engineering parameters at thousands of locations along optical sensing fibers where weakly reflecting Bragg gratings have been photoetched. Application of the sensing fibers outside of the development lab has revealed several areas for improvement. Some of the problems encountered include polarization fading, non-linear laser tuning, and sensor calibration. This paper considers the use of polarization diversity detection and monitoring of the laser tuning characteristics to provide a more robust OFDR system for both sensor calibration and measurement. Possible modifications to the system are reported along with calibration measurements for quantifying the effects of polarization fading in the sensing fiber.
Microscopic Viscoelasticity: Shear Moduli of Soft Materials Determined from Thermal Fluctuations (1997)

We describe a high-resolution, high-bandwidth technique for determining the local viscoelasticity of soft materials such as polymer gels. Loss and storage shear moduli are determined from the power spectra of thermal fluctuations of embedded micron-sized probe particles, observed with an interferometric microscope. This provides a passive, small-amplitude measurement of rheological properties over a much broader frequency range than previously accessible to microrheology. We study both F-actin biopolymer solutions and polyacrylamide (PAAm) gels, as model semiflexible and flexible systems, respectively. We observe high-frequency ${\ensuremath{\omega}}^{3/4}$ scaling of the shear modulus in F-actin solutions, in contrast to ${\ensuremath{\omega}}^{1/2}$ scaling for PAAm.
A multi-level study of recombinant Pichia pastoris in different oxygen conditions (2010)

This systems level study helped to understand the physiological adaptations of cellular mechanisms to low oxygen availability in a recombinant P. pastoris strain. Remarkably, the integration of data from three different levels allowed for the identification of differences in the regulation of the core metabolism between P. pastoris and S. cerevisiae. Detailed comparative analysis of the transcriptomic data also led to new insights into the gene expression profiles of several cellular processes that are not only susceptible to low oxygen concentrations, but might also contribute to enhanced protein secretion.
Enhancing Chemotherapy Response with Sustained EphA2 Silencing Using Multistage Vector Delivery (2013)

These findings indicate that MSV/EphA2 merits further development as a novel therapeutic agent for ovarian cancer.
Novel African Trypanocidal Agents: Membrane Rigidifying Peptides (2012)

The bloodstream developmental forms of pathogenic African trypanosomes are uniquely susceptible to killing by small hydrophobic peptides. Trypanocidal activity is conferred by peptide hydrophobicity and charge distribution and results from increased rigidity of the plasma membrane. Structural analysis of lipid-associated peptide suggests a mechanism of phospholipid clamping in which an internal hydrophobic bulge anchors the peptide in the membrane and positively charged moieties at the termini coordinate phosphates of the polar lipid headgroups. This mechanism reveals a necessary phenotype in bloodstream form African trypanosomes, high membrane fluidity, and we suggest that targeting the plasma membrane lipid bilayer as a whole may be a novel strategy for the development of new pharmaceutical agents. Additionally, the peptides we have described may be valuable tools for probing the biosynthetic machinery responsible for the unique composition and characteristics of African trypanosome plasma membranes.
Semantic depth of field (2005)

We present a new technique called Semantic Depth of Field (SDOF) as an alternative approach to focus-and-context displays of information. We utilize a well-known method from photography and cinematography (depth-of-field effect) for information visualization, which is to blur different parts of the depicted scene in dependence of their relevance. Independent of their spatial locations, objects of interest are depicted sharply in SDOF, whereas the context of the visualization is blurred. In this paper, we present a flexible model of SDOF which can be easily adopted to various types of applications. We discuss pros and cons of the new technique, give examples of application, and describe a fast prototype implementation of SDOF.
Oxygen optrode for use in a fiber-optic glucose biosensor (1990)

An optical fiber oxygen sensor, based on the dynamic quenching of the luminescence of tris(1,10-phenanthroline)-ruthenium(II) cation by molecular oxygen, is presented. The complex is adsorbed onto silica gel, incorporated in a silicone matrix possessing a high oxygen permeability, and placed at the tip of the optical fiber. Oxygen has been monitored continuously in the 0-750 Torr range, with the detection limit being as low as 0.7 Torr. The device has been applied to the development of a fast responding and highly sensitive fiber-optic glucose biosensor based on this highly sensitive oxygen transducer. The sensor relates oxygen consumption (as a result of enzymatic oxidation) to glucose concentration. The enzyme is immobilized on the surface of the oxygen optrode; carbon black is used as an optical isolation in order to prevent ambient light and sample fluorescence to interfere. Measurements have been performed in a flow-through cell in air-equilibrated glucose standard solutions of pH 7.0. The effects of enzyme immobilization procedures (including enzyme immobilization on carbon black) as to response times (around 6 min), analytical ranges (0.06-1 mM glucose), reproducibility in sensor construction, and long-term stability have been studied as well.
The nigrostriatal system in Parkinson's disease. (1990)

Patterns of dopaminergic cell loss in the midbrain and patterns of mesostriatal fiber loss in the caudate nucleus and putamen are described for cases of idiopathic Parkinson's disease. Neither cell loss nor fiber loss is homogeneous. In the midbrain, quantitative analysis points to a selective vulnerability of neurons in the most heavily pigmented dopaminergic cell groups. In the striatum, a dorsolateral-to-ventromedial gradient of loss appears to characterize both the caudate nucleus and the putamen. These patterns of loss and sparing have implications both for analysis of the clinical symptoms of Parkinson's disease and for study of the etiology of this disease.
SEMI E133—The Process Control System Standard: Deriving a Software Interoperability Standard for Advanced Process Control in Semiconductor Manufacturing (2007)

The process control systems (PCS) SEMI Standard E133 facilitates the integration of PCS into current and future fabs. The standard focuses on defining the portion of ldquointerface Brdquo associated with communication with and between components of PCSs. Specifically, the scope of the standard is the functional groups of run-to-run (R2R) control, fault detection (FD), fault classification (FC), fault prediction (FP), and statistical process control (SPC). The standard specifies PCS interfaces (which utilize ldquointerface Brdquo) that will enable these functional groups to interact effectively and share data among themselves and with the other interdependent factory systems, including systems within the process equipment. Key requirements driving the standard specification include the move to service-oriented and event-driven architectures and a need to define PCS capabilities from an input/output (I/O) perspective along functional boundaries defined by commercial applications. The developed standard addresses these requirements and specifies: 1) the capabilities of all five functional groups; 2) a comprehensive I/O interface data model; 3) an XML representation of that data model (E133.1); 4) a set of common services and behavior classes; 5) extensions of the I/O structure and behavior for each functional group; and 6) an application note that provides an example of PCS integration with equipment data acquisition (EDA) data collection. XML, R2R control, and FD implementation examples illustrate that the standard addresses these requirements, with the FD example further illustrating compatibility with EDA ldquointerface Ardquo standards. The standard to date has mature R2R control and FD specifications with key PCS users and providers indicating that they are using the standard extensively.
Audible noise and losses in variable speed induction motor drives with IGBT inverters-influence of the squirrel cage design and the switching frequency (2002)

This paper describes a large number of experiments comparing audible noise, losses and efficiency of different induction motors supplied by an IGBT inverter. The influence of the switching frequency on the motor behaviour is analysed. As a comparison the motor is also supplied directly from the mains. Furthermore two different motors are compared to study the influence of the rotor cage design on the motor behaviour. It is shown that the choice of the switching frequency has a large influence on the audible noise produced by induction motors. By taking higher switching frequencies, the time harmonics move to a nonaudible region. At some higher switching frequencies subharmonics appear, having a bad influence on the audible noise. At higher fundamental frequencies the audible noise of the fan dominates. The switching frequencies can cause pure tones that are very disturbing to the human ear. The influence of the switching frequency on the efficiency is rather small. Minimal overall losses appear around 3 and 4 kHz. The voltage-frequency ratio should be taken constant from the point of view of the efficiency.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Simultaneous assessment of key properties of arid soil by combined PXRF and V is– NIR data (2016)

Summary Arid soil is common worldwide and has unique properties that often limit agronomic productivity, specifically, salinity expressed as soluble salts and large amounts of calcium carbonate and gypsum. Currently, the most common methods for evaluating these properties in soil are laboratory‐based techniques such as titration, gasometry and electrical conductivity. In this research, we used two proximal sensors (portable X ‐ray fluorescence ( PXRF ) and visible near‐infrared diffuse reflectance spectroscopy ( V is– NIR DRS )) to scan a diverse set ( n = 116) of samples from arid soil in S pain. Then, samples were processed by standard laboratory procedures and the two datasets were compared with advanced statistical techniques. The latter included penalized spline regression ( PSR ), support vector regression ( SVR ) and random forest ( RF ) analysis, which were applied to V is– NIR DRS data, PXRF data and PXRF and V is– NIR DRS data, respectively. Independent validation (30% of the data) of the calibration equations showed that PSR + RF predicted gypsum with a ratio of performance to interquartile distance ( RPIQ ) of 5.90 and residual prediction deviation ( RPD ) of 4.60, electrical conductivity (1:5 soil : water) with RPIQ of 3.14 and RPD of 2.10, C a content with RPIQ of 2.92 and RPD of 2.07 and calcium carbonate equivalent with RPIQ of 2.13 and RPD of 1.74. The combined PXRF and V is– NIR DRS approach was superior to those that use data from a single proximal sensor, enabling the prediction of several properties from two simple, rapid, non‐destructive scans.
Monoclonal B-Cell Lymphocytosis and Chronic Lymphocytic Leukemia (2008)

The CLL-phenotype cells found in the general population and in subjects with lymphocytosis have features in common with CLL cells. CLL requiring treatment develops in subjects with CLL-phenotype MBL and with lymphocytosis at the rate of 1.1% per year.
Antiplatelet properties of protein S-nitrosothiols derived from nitric oxide and endothelium-derived relaxing factor. (1993)

S-nitrosothiols may serve as carriers in the mechanism of action of endothelium-derived relaxing factor (EDRF) by stabilizing the labile nitric oxide (NO) radical from inactivation by reactive species in the physiological milieu and by delivering NO to the heme activator site of guanylyl cyclase. Low-molecular-weight thiols, such as cysteine and glutathione, form S-nitrosothiol adducts with vasodilatory and antiplatelet properties, and protein thiols can interact in the presence of NO and/or EDRF to form uniquely stable S-nitroso-proteins. We now show that the S-nitroso-proteins, S-nitroso-albumin, S-nitroso-tissue type plasminogen activator, and S-nitroso-cathepsin B, have potent antiplatelet effects with an IC50 of approximately 1.5 microM. In the dog, S-nitroso-albumin inhibits ex vivo platelet aggregation and significantly prolongs the template bleeding time from 2.15 +/- 0.13 (mean +/- SEM) to 9.70 +/- 1.24 minutes. The antiplatelet action of S-nitroso-proteins is associated with the stimulation of guanylyl cyclase and a significant decrease in fibrinogen binding to platelets. S-Nitroso-proteins undergo thiol-nitrosothiol exchange with low-molecular-weight thiols to form low-molecular-weight S-nitroso-thiols, and they also interact directly with the platelet surface, both of which processes facilitate generation of NO. These data suggest that S-nitroso-proteins are potent antiplatelet agents and may be intermediates in the antiplatelet mechanism of EDRF action.
Relationships Among the Composition of Mucus, Epithelial Lining Liquid, and Adhesion of Microorganisms (1995)

Airway surface liquid (ASL) is complex and comes from many sources, in particular glands and epithelium. The mucoglycoproteins present bind to bacteria. Bacterial membranes contain adhesins that bind to receptors on the mucus. The bound bacteria multiply and release toxins that diffuse to the epithelium and damage or destroy it, inhibiting mucociliary transport. The damaged epithelium releases products such as phospholipids into the ASL. These change the physical properties of the mucus and also promote mucus secretion, which may block smaller airways. Airway surface liquid contains constituents such as immunoglobulins, lysozyme, and lactoferrin and neutrophil products such as proteases that act on bacteria. Few bacteria adhere to healthy epithelium. To adhere, most require damaged tissue with membrane receptors that encourage bacterial invasion. If the epithelium is destroyed, bacteria adhere to the basement membrane or extracellular matrix. A damaged epithelium can also cause hyperresponsiveness of airway secretory mechanisms, with increased gland secretion that in turn interacts with the bacteria.
An experimental comparison of naive Bayesian and keyword-based anti-spam filtering with personal e-mail messages (2000)

The growing problem of unsolicited bulk e-mail, also known as “spam”, has generated a need for reliable anti-spam e-mail filters. Filters of this type have so far been based mostly on manually constructed keyword patterns. An alternative approach has recently been proposed, whereby a Naive Bayesian classifier is trained automatically to detect spam messages. We test this approach on a large collection of personal e-mail messages, which we make publicly available in “encrypted” form contributing towards standard benchmarks. We introduce appropriate cost-sensitive measures, investigating at the same time the effect of attribute-set size, training-corpus size, lemmatization, and stop lists, issues that have not been explored in previous experiments. Finally, the Naive Bayesian filter is compared, in terms of performance, to a filter that uses keyword patterns, and which is part of a widely used e-mail reader.
Human IL-7: a novel T cell growth factor. (1989)

Abstract IL-7 is a hemopoietic growth factor that induces the proliferation of early B lineage cells. In the course of studies to determine its effect on human bone marrow cells, we noted a marked outgrowth of mature T cells. When T cells from the circulation were cultured with IL-7, a dose-dependent proliferative response was observed. The target cells included both the CD4+ and CD8+ subpopulations of T cells, but the memory T cells (CD45R-) were better responders than unprimed T cells (CD45R+). IL-7 induced the expression of receptors for IL-2 and transferrin and higher levels of the 4F2 activation Ag. Although T cell responses to suboptimal concentrations of IL-7 were enhanced by the addition of IL-2, the proliferative response to IL-7 was not inhibited by neutralizing antibody to the IL-2R (Tac), nor was IL-2 secretion detected in this response. This response pattern of mature T cells suggests an important role for IL-7 in normal T cell physiology in humans.
The Relative Binding Affinities of PDZ Partners for CFTR: A Biochemical Basis for Efficient Endocytic Recycling (2008)

The cystic fibrosis transmembrane conductance regulator (CFTR) is an epithelial chloride channel mutated in patients with cystic fibrosis. Its expression and functional interactions in the apical membrane are regulated by several PDZ (PSD-95, discs large, zonula occludens-1) proteins, which mediate protein-protein interactions, typically by binding C-terminal recognition motifs. In particular, the CFTR-associated ligand (CAL) limits cell-surface levels of the most common disease-associated mutant DeltaF508-CFTR. CAL also mediates degradation of wild-type CFTR, targeting it to lysosomes following endocytosis. Nevertheless, wild-type CFTR survives numerous cycles of uptake and recycling. In doing so, how does it repeatedly avoid CAL-mediated degradation? One mechanism may involve competition between CAL and other PDZ proteins including Na (+)/H (+) exchanger-3 regulatory factors 1 and 2 (NHERF1 and NHERF2), which functionally stabilize cell-surface CFTR. Thus, to understand the biochemical basis of WT-CFTR persistence, we need to know the relative affinities of these partners. However, no quantitative binding data are available for CAL or the individual NHERF2 PDZ domains, and published estimates for the NHERF1 PDZ domains conflict. Here we demonstrate that the affinity of the CAL PDZ domain for the CFTR C-terminus is much weaker than those of NHERF1 and NHERF2 domains, enabling wild-type CFTR to avoid premature entrapment in the lysosomal pathway. At the same time, CAL's affinity is evidently sufficient to capture and degrade more rapidly cycling mutants, such as DeltaF508-CFTR. The relatively weak affinity of the CAL:CFTR interaction may provide a pharmacological window for stabilizing rescued DeltaF508-CFTR in patients with cystic fibrosis.
Current understanding of the structure, phase transitions and dynamics of self-assembled monolayers on two- and three-dimensional surfaces (2003)

Self-assembled monolayers (SAMs) have been the preferred material systems to investigate specific properties in several disciplines for nearly 15 years. Advances in various techniques and their application to the study of SAMs have dramatically improved our understanding of these systems. Adaptation of this molecular architecture into three dimensions in the form of monolayer-protected clusters enabled the use of bulk techniques for the study of monolayers. Here we review recent developments in the structural properties and temperature-induced phase transitions of both these SAM structures. While alkanethiols on Au (111) and Ag (111) are taken as archetypal systems to discuss the properties of SAMs on two-dimensional surfaces, their assemblies on Au and Ag cluster surfaces are taken as examples for SAMs on three-dimensional surfaces. A comparison of these two SAMs is provided.
Traumatic Brain Injury (2002)

Animal models have played a critical role in elucidating the complex pathogenesis of traumatic brain injury, the major cause of death and disability in young adults in Western countries. This review discusses how different types of animal models are useful for the study of neuropathologic processes in traumatic, blunt, nonmissile head injury.
Design of P1‘ and P3‘ Residues of Trivalent Thrombin Inhibitors and Their Crystal Structures (2000)

Synthetic bivalent thrombin inhibitors comprise an active site blocking segment, a fibrinogen recognition exosite blocking segment, and a linker connecting these segments. Possible nonpolar interactions of the P1' and P3' residues of the linker with thrombin S1' and S3' subsites, respectively, were identified using the "Methyl Scan" method [Slon-Usakiewicz et al. (1997) Biochemistry 36, 13494-13502]. A series of inhibitors (4-tert-butylbenzenesulfonyl)-Arg-(D-pipecolic acid)-Xaa-Gly-Yaa-Gly-betaAla-Asp-Tyr-Glu-Pro-Ile-Pro-Glu-Glu-Ala- (be ta-cyclohexylalanine)-(D-Glu)-OH, in which nonpolar P1' residue Xaa or P3' residue Yaa was incorporated, were designed and improved the affinity to thrombin. Substitution of the P3' residue with D-phenylglycine or D-Phe improved the K(i) value to (9.5 +/- 0.6) x 10(-14) or 1.3 +/- 0.5 x 10(-13) M, respectively, compared to that of a reference inhibitor with Gly residues at Xaa and Yaa residues (K(i) = (2.4 +/- 0.5) x 10(-11) M). Similarly, substitution of the P1' residue with L-norleucine or L-beta-(2-thienyl)alanine lowered the K(i) values to (8.2 +/- 0.6) x 10(-14) or (5.1 +/- 0.4) x 10(-14) M, respectively. The linker Gly-Gly-Gly-betaAla of the inhibitors in the previous sentence was simplified with 12-aminododecanoic acid, resulting in further improvement of the K(i) values to (3.8 +/- 0.6) x 10(-14) or (1.7 +/- 0.4) x 10(-14) M, respectively. These K(i) values are equivalent to that of natural hirudin (2.2 x 10(-14) M), yet the size of the synthetic inhibitors (2 kD) is only one-third that of hirudin (7 kD). Two inhibitors, with L-norleucine or L-beta-(2-thienyl)alanine at the P1' residue and the improved linker of 12-aminododecanoic acid, were crystallized in complex with human alpha-thrombin. The crystal structures of these complexes were solved and refined to 2.1 A resolution. The Lys(60F) side chain of thrombin moved significantly and formed a large nonpolar S1' subsite to accommodate the bulky P1' residue.