gebhart/patrepeval huggingface dataset:
Proximity x-ray lithography of siloxane and polymer films containing benzyl chloride functional groups (1999)

Silicon wafers coated with films of (p-chloromethyl)phenyl-trichlorosilane or spun coated polyvinyl benzyl chloride were exposed at the University of Wisconsin synchrotron x-ray source using 0.9385 nm radiation (800 MeV) at doses ranging from 50 to 1500 mJ/cm2. Exposure resulted in changes to the surface energy and chemical reactivity of the films. The loss of chlorine and formation of oxidized carbon photoproducts upon exposure was followed as a function of dose using x-ray photoelectron spectroscopy. A corresponding change in surface energy, as monitored by static water contact angle, was also observed. The selective chemical grafting (reductive amination) of amine ligands to the portions of the siloxane and polymer films which have been exposed to proximity x rays definitively establishes the formation of surface aldehyde or ketone groups as an important photochemical pathway. The resulting surface amine was used to covalently bind either a fluorescent tag or a colloidal Pd (II) nanoparticle capable of initiating the selective deposition of electroless Ni in the irradiated regions of the film.
The T cell response of HLA-DR transgenic mice to human myelin basic protein and other antigens in the presence and absence of human CD4. (1995)

Analysis of HLA class II transgenic mice has progressed in recent years from analysis of single chain HLA class II transgenes with expression of mixed mouse/human heterodimers to double transgenic mice expressing normal human heterodimers. Previous studies have used either HLA transgenic mice in which there is a species-matched interaction with CD4 or mice which lack this interaction. Since both systems are reported to generate HLA-restricted responses, the matter of the requirement for species-matched CD4 remains unclear. We have generated triple transgenic mice expressing three human transgenes, DRA, DRB, and CD4, and compared HLA-restricted responses to peptide between human-CD4+ (Hu-CD4+) and Hu-CD4- littermates. We saw no difference between Hu-CD4+ and Hu-CD4- groups, supporting the notion that for some responses at least the requirement for species-matched CD4 may not be absolute. Evidence for positive selection of mouse T cell receptors in HLA-DR transgenic mice came both from the acquisition of new, HLA-restricted responses to various peptides and from an increased frequency of T cells using the TCR V beta 4 gene segment. An important goal with respect to the analysis of function in HLA transgenic mice is the clarification of mechanisms which underpin the recognition of self-antigens in human autoimmune disease. As a first step towards 'humanized' disease models in HLA transgenic mice, we analyzed the responses of HLA-DR transgenic mice to the human MPB 139-154 peptide which has been implicated as an epitope recognized by T cells of multiple sclerosis patients. We obtained T cell responses to this epitope in transgenic mice but not in nontransgenic controls. This study suggests that HLA transgenic mice will be valuable in the analysis of HLA-restricted T cell epitopes implicated in human disease and possibly in the design of new disease models.
Endotoxin stimulates gene expression of ROS-eliminating pathways in rat hepatic endothelial and Kupffer cells (1996)

Reactive oxygen species (ROS) are mediators of cellular injury and play a putative role in the onset of hepatic damage during endotoxemia or sepsis. It has been suggested that induction of glucose-6-phosphate (G-6-P) dehydrogenase, the key enzyme of the hexose monophosphate shunt (HMS), may support ROS-producing or ROS-eliminating pathways in hepatic endothelial and Kupffer cells during endotoxemia. The aim of the study was to assess in vivo lipopolysaccharide (LPS)-induced alterations in rat gene expression of selected enzymes that are in functional relationship with the HMS. mRNA levels and activities of glucose transporter GLUT-1, Mn- and CuZn-dependent superoxide dismutases (Mn-SOD and CuZn-SOD), and Se-dependent glutathione peroxidase (Se-GPX) were determined. Cellular extracts were analyzed 7 or 22 h after injection of LPS (Escherichia coli, 2 mg/kg ip) or injection of saline. Exposure to LPS for 7 or 22 h caused a 10- to 25-fold increase in GLUT-1 mRNA levels in endothelial and Kupffer cells. In parenchymal cells, GLUT-1 mRNA expression was low, and LPS caused no marked changes. Cellular levels of Mn-SOD mRNA were 20-40 times greater in all hepatic cells from LPS-treated animals than in cells from control rats. LPS at 22 h increased Mn-SOD activity by 45% in endothelial cells but caused no significant changes in Kupffer or parenchymal cells. Message levels and enzyme activities of CuZn-SOD and Se-GPX were significantly elevated 22 h after LPS injection in endothelial cells only. Thus LPS results in marked upregulation of functionally related genes in hepatic cells. In endothelial cells, the simultaneous upregulation of GLUT-1, G-6-P dehydrogenase, Mn-SOD, CuZn-SOD, and Se-GPX may represent an important mechanism for accelerated elimination of ROS released from activated sinusoidal phagocytes. In Kupffer cells, upregulated GLUT-1 and G-6-P dehydrogenase, together with constitutively present SOD and lack of upregulated Se-GPX, suggest an elevated capacity to produce O2- and H2O2 that is consistent with primed bacterial killing.
NLRP3 inflammasome activation is associated with proliferative diabetic retinopathy (2017)

Abstract Purpose Innate immunity and dysregulation of inflammatory processes play a role in vascular diseases like atherosclerosis or diabetes. Nucleotide‐binding domain and Leucine‐rich repeat Receptor containing a Pyrin domain 3 ( NLRP 3) inflammasomes are pro‐inflammatory signalling complexes that were found in 2002. In addition to pathogens and other extracellular threats, they can be activated by various endogenous danger signals. The purpose of this study was to find out whether NLRP 3 activation occurs in patients with sight‐threatening forms of diabetic retinopathy ( DR ). Methods Inflammasome components NLRP 3 and caspase‐1, inflammasome‐related pro‐inflammatory cytokines IL ‐1 β and IL ‐18, vascular endothelial growth factor ( VEGF ), acute‐phase cytokines TNF ‐ α and IL ‐6, as well as adaptive immunity‐related cytokine interferon gamma ( IFN ‐ γ ) were measured from the vitreous samples of 15 non‐proliferative diabetic retinopathy (non‐ PDR ) and 23 proliferative diabetic retinopathy (PDR) patients using the enzyme‐linked immunosorbent assay ( ELISA ) method. The adaptor protein apoptosis‐associated speck‐like protein containing a CARD (ASC) was determined using the Western blot technique. Results Inflammasome components were present in the vitreous of DR patients. Along with VEGF , the levels of caspase‐1 and IL ‐18 were significantly increased, especially in PDR eyes. Interestingly, clearly higher levels of NLRP 3 were found in the PDR eyes with tractional retinal detachment ( TRD ) than from PDR eyes with fully attached retina. There were no significant differences in the amounts of IL ‐1 β , TNF ‐ α , IL ‐6, and IFN ‐ γ that were detectable in the vitreous of both non‐ PDR and PDR patients. Conclusion Our results suggest that NLRP 3 inflammasome activation can be associated especially with the pathogenesis of PDR . The lack of differences in TNF ‐ α , IL ‐6, and IFN ‐ γ also alludes that acute inflammation or T‐cell‐mediated responses do not dominate in PDR pathogenesis.
Structural Determination of Bulk and Surface Tungsten Oxides with UV−vis Diffuse Reflectance Spectroscopy and Raman Spectroscopy (2007)

Combined UV−vis diffuse reflectance spectroscopy (DRS) and Raman spectroscopy were applied to examine the electronic and molecular structures, respectively, of well-defined W(VI) bulk mixed oxide reference compounds consisting of (i) isolated WO4 or WO6 monomers, (ii) dimeric O3W−O−WO3, (iii) polymeric chain of alternating WO4/WO6 units, and (iv) WO6-coordinated W9−W18 clusters. Raman spectroscopy was employed to confirm the identity and phase purity of the different tungsten oxide structures. UV−vis DRS provided the corresponding electronic edge energy (Eg) of the ligand-to-metal charge transfer (LMCT) transitions of the W(VI) cations. A correlation between the edge energy and the number of covalent bridging W−O−W bonds around the central W(VI) cation was found with Eg linearly decreasing with increasing number of bridging W−O−W bonds. However, a direct relationship between Eg and the domain size, NW, for finite WOx clusters does not exist. Subsequently, UV−vis and Raman spectroscopy information were applied to determine the local structures of the molecularly dispersed surface W(VI) species present in supported WO3/Al2O3, WO3/ZrO2, and WO3/SiO2 catalysts under ambient and dehydrated conditions.
Growth of AlN films and their characterization (2006)

Abstract Single crystal AlN layers have been produced by migration enhanced metal organic chemical vapor deposition (MEMOCVD), hydride vapor phase epitaxy (HVPE) and their combination. The growth was carried out on 2” basal plane sapphire substrates. In MEMOCVD, the duration and waveforms of precursors were varied to achieve better surface mobility and thus better atomic incorporation. It resulted in superior layer quality templates with the narrowest (002) X‐ray rocking curve full width half maximum (FWHM). Such high quality AlN templates were used as seeds for subsequent HVPE growth. Thick films with thickness ranging from 1‐25 µm have been grown by HVPE with growth rates as high as 200 µm/min, highest ever reported. Films grown by the two methods have been extensively characterized by Nomarski microscopy, scanning electron microscopy (SEM), atomic force microscopy (AFM), high‐resolution X‐ray diffractometry (HRXRD), and photoluminescence (PL). (© 2006 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Aspirin for the Primary Prevention of Cardiovascular Events: An Update of the Evidence for the U.S. Preventive Services Task Force (2009)

Aspirin reduces the risk for myocardial infarction in men and strokes in women. Aspirin use increases the risk for serious bleeding events.
Experience with transdermal testosterone replacement therapy for hypogonadal men (1999)

Adverse events were substantially higher than reported from clinical trials but in keeping with the spectrum of yellow card reports received by the Committee on Safety of Medicines. The pharmacokinetic advantages are thus largely outweighed by low patient acceptability. In its present form transdermal therapy remains an expensive option for those who cannot tolerate depot testosterone replacement.
Dynamics of the Human Masticatory System (2002)

In this review, the movement characteristics of the human masticatory system are discussed from a biomechanical perspective. The discussion is based upon the three fundamental laws of mechanics applied to the various anatomical structures that are part of the masticatory system. An analysis of the forces and torques applied to the mandible by muscles, joints, articular capsules, and teeth is used to assess the determinants of jaw movement. The principle of relating the interplay of forces to the center of gravity of the lower jaw, in contrast to a hinge axis near its joints, is introduced. It is evident that the muscles are the dominant determinants of jaw movement. The contributions of the individual muscles to jaw movements can be derived from the orientation of their lines of action with respect to the center of gravity of the lower jaw. They cause the jaw to accelerate with six degrees of freedom. The ratio between linear and angular accelerations is subtly dependent on the mass and moments of inertia of the jaw, and the structures that are more or less rigidly attached to it. The effects of articular forces must be taken into account, especially if the joints are loaded asymmetrically. The muscles not only move the jaw but also maintain articular stability during midline movements. Passive structures, such as the ligaments, become dominant only when the jaw reaches its movement boundaries. These ligaments are assumed to prevent joint dislocation during non-midline movements.
Evaluation of the probe 2',7'-dichlorofluorescin as an indicator of reactive oxygen species formation and oxidative stress (1992)

The use of dichlorofluorescin (DCFH) as a measure of reactive oxygen species was studied in aqueous media. Hydrogen peroxide oxidized DCFH to fluorescent dichlorofluorescein (DCF), and the oxidation was amplified by the addition of ferrous iron. Hydrogen peroxide-induced DCF formation in the presence of ferrous iron was completely inhibited by deferoxamine and partially inhibited by ethylenediaminetetraacetic acid, but was augmented by diethylenetriaminepentaacetic acid. Iron-peroxide-induced oxidation of DCFH was partially inhibited by catalase but not by horseradish peroxidase. Nonchelated iron-peroxide oxidation of DCFH was partially inhibited by several hydroxyl radical scavengers, but was independent of the scavenger concentration, and this suggests that free hydroxyl radical is not involved in the oxidation of DCFH in this system. Superoxide anion did not directly oxidize DCFH. Data suggest that H2O2-Fe(2+)-derived oxidant is mainly responsible for the nonenzymatic oxidation of DCFH. In addition, peroxidase alone and oxidants formed during the reduction of H2O2 by peroxidase oxidize DCFH. Since DCFH oxidation may be derived from several reactive intermediates, interpretation of specific reactive oxygen species involved in biological systems should be approached with caution. However, DCFH remains an attractive probe as an overall index of oxidative stress in toxicological phenomena.
Blocking P‐selectin protects from ischemia/reperfusion‐induced acute renal failure (2000)

Acute renal failure (ARF) in response to ischemia-reperfusion is thought to be associated with neutrophil infiltration. Neutrophil recruitment depends on adhesion molecules, including P-selectin. Our study sought to characterize the role of P-selectin in ischemia-reperfusion (I/R) -induced acute renal failure (ARF). In wild-type (wt) and P-selectin-deficient (P-/-) mice (both C57BL/6), ARF was induced by 32 min bilateral renal ischemia, followed by reperfusion (I/R). Wt showed a 12- and 20-fold increase in creatinine at 24 and 48 h after I/R, respectively. Similar changes were seen in blood urea nitrogen (BUN). By contrast, in P-/- creatinine and BUN increased only moderately (fourfold over sham). In wt, renal myeloperoxidase activity, indicating neutrophil infiltration, peaked after 24 h (19-fold over sham). This was significantly attenuated in P-/- (fivefold over sham). Western blot analysis revealed maximum P-selectin expression 12 h after I/R in wt. Immunostaining detected P-selectin in glomerular endothelium and in platelets adherent in glomerular and peritubular vessels. Postischemic injection of P-selectin antibody at 10 min after reperfusion, but not isotype control antibody, protected wt from ARF similar to the protection seen in P-/-. We conclude that blocking P-selectin even after onset of reperfusion protects mice from I/R-induced ARF, suggesting potential therapeutic strategies aimed at blocking P-selectin.
The Purification and Properties of Sucrose Synthetase from Etiolated Phaseolus aureus Seedlings (1972)

Abstract UDP-glucose:d-fructose 2-glucosyltransferase (EC 2.4.1.14), commonly called sucrose synthetase, has been purified from etiolated Phaseolus aureus seedlings to homogeneity by electrophoretic, immunological, and ultracentrifugal criteria. Molecular weight determinations by low speed equilibrium centrifugation yields a value of 375,000 ± 12,000. A value of 405,000 ± 20,000 was obtained by gel filtration. Other physical determinations for the enzyme yielded the following data: s20,w = 12.4 x 10-13 sec-1; diffusion constant (D20,w) = 3.03 x 10-7 cm-2 sec-1; and f/f0 = 1.49. Subunit analyses indicate that the enzyme is a tetramer composed of identical protein subunits of approximate molecular weight 94,000. An equilibrium constant of 0.15 for the sucrose synthetase reaction at pH 7.5 and 25° in the direction of uridine diphosphate glucose synthesis was experimentally determined. The kinetic parameters of the enzyme in the proposed physiological direction, that of nucleoside diphosphate glucose synthesis, have been measured. When UDP is present at saturating levels, the Km for sucrose was determined to be 17 mm. A similar value (29 mm) was obtained when ADP was the second substrate. Upon complete purification the enzyme retains activity for UDP, ADP, TDP, CDP, or GDP as substrates. Km values for these substrates, determined in the presence of saturating sucrose, are 0.19, 0.19, 0.30, 0.44, and 0.17 mm, respectively. The Vmax in the presence of these substrates are, in relative numbers, 100, 28.6, 5.8, 3.4, and 2.8, respectively. Kinetic data indicate a random mechanism for the enzyme.
Longitudinal PET Evaluation of Cerebral Metabolic Decline in Dementia: A Potential Outcome Measure in Alzheimer’s Disease Treatment Studies (2002)

These findings indicate that brain metabolism as assessed by FDG PET during mental rest is a sensitive marker of disease progression in Alzheimer's disease over a 1-year period. These findings also support the feasibility of using FDG PET as an outcome measure to test the ability of treatments to attenuate the progression of Alzheimer's disease.
Dynamics of UUV Umbilical Cables - Computer Simulation and Experimental Measurements (2002)

The Advantage of Uninhabited Undersea Vehicles (UUVs) is that they can be used to perform dangerous or time-dependent operations where a human presence is either not safe or not practical. UUVs are therefore uniquely suited to providing a standoff capability for undersea ordnance identification and mine disposal, and to conduct clandestine reconnaissance and surveillance missions in support of amphibious operations. DSTO manages a research program focused on the exploitation of UUVs and associated technologies to deliver advanced military capabilities. DSTO has developed its own UUV for use as a test-bed for proving system concepts and validating new technologies for submarines and minehunting platforms. DSTO also manages a project aimed at maximizing the operational effectiveness and system performance of the BOFORS Double Eagle Mine Disposal System, which is in service on the Huon Class Minehunter Coastal Vessels. A major aspect of this project is the application of modelling and simulation, which includes the development of computationally efficient dynamic models for real time and human-in-the-loop computer systems. These models will play am important role in the development and validation of advanced controllers for station keeping and manoeuvring and when the vehicle is retrofitted with new sensor payloads. It is envisaged that these models may be carried through to demonstration as operational tools for mission planning or for improving pilot situation awareness.
Ultrasensitivity and noise propagation in a synthetic transcriptional cascade (2005)

The precise nature of information flow through a biological network, which is governed by factors such as response sensitivities and noise propagation, greatly affects the operation of biological systems. Quantitative analysis of these properties is often difficult in naturally occurring systems but can be greatly facilitated by studying simple synthetic networks. Here, we report the construction of synthetic transcriptional cascades comprising one, two, and three repression stages. These model systems enable us to analyze sensitivity and noise propagation as a function of network complexity. We demonstrate experimentally steady-state switching behavior that becomes sharper with longer cascades. The regulatory mechanisms that confer this ultrasensitive response both attenuate and amplify phenotypical variations depending on the system's input conditions. Although noise attenuation allows the cascade to act as a low-pass filter by rejecting short-lived perturbations in input conditions, noise amplification results in loss of synchrony among a cell population. The experimental results demonstrating the above network properties correlate well with simulations of a simple mathematical model of the system.
Construction of filter vectors for the information-efficient spectral imaging sensor (1998)

The information-efficient spectral imaging sensor (ISIS) seeks to improve system performance by processing hyperspectral information in the optical hardware. Its output may be a gray scale image in which one attempts to maximize the contrast between a given target and the background. Alternatively, its output may be a small number of images, rather than a full data cube, that retain the essential information required in the application. The principal advantage of ISIS is that it offers the discrimination of hyperspectral imaging while achieving the signal-to-noise ratio of multispectral imaging. The paper focuses on construction of the filter vectors that are needed to program ISIS. The instrument produces an image which is essentially a dot product of the scene and the filter vector. Both single vector and multiple vector approaches are considered. Also, they discuss some subtle points related to optimizing the filter vectors.
Improved Ion Transmission from Atmospheric Pressure to High Vacuum Using a Multicapillary Inlet and Electrodynamic Ion Funnel Interface (2000)

A heated multicapillary inlet and ion funnel interface was developed to couple an electrospray ionization (ESI) source to a high-vacuum stage for obtaining improved sensitivity in mass spectrometric applications. The inlet was constructed from an array of seven thin-wall stainless steel tubes soldered into a central hole of a cylindrical heating block. An electrodynamic ion funnel was used in the interface region to more effectively capture, focus, and transmit ions from the multicapillary inlet. The interface of seven capillary inlets with the ion funnel showed more than 7 times higher transmission efficiency compared to that of a single capillary inlet with the ion funnel and a 23-fold greater transmission efficiency than could be obtained using the standard orifice-skimmer interface of a triple-quadrupole MS. The multiple-capillary inlet and ion funnel interface showed an overall 10% ion transmission efficiency and approximately 3-4% overall detection efficiency of ions from solution based (i.e., prior to electrospray). The improved performance was achieved under conditions where ESI operation is robust and results in a significant increase in dynamic range.