gebhart/patrepeval huggingface dataset:
Exogenous Epidermal Growth Factor Fails to Accelerate Functional Recovery in the Autotransplanted Ischemic Pig Kidney (1993)

The reversibility of ischemic renal injury is dependent on epithelial cell regeneration and repopulation of the nephron. Renal cells produce and respond to many growth factors. In the rat, epidermal growth factor (EGF) is mitogenic for tubular cells and accelerates renal recovery after ischemia. We used a pig renal autotransplant model to evaluate the effect of exogenous EGF on renal recovery in a large animal more analogous to man. Group 1 animals underwent left autotransplant after 120 minutes of warm ischemia and received either a single intra-arterial dose of recombinant human EGF (EGF, 10(-7) M.) (N = 11) or vehicle alone (N = 6). Group 2 animals underwent left autotransplant after 72 hours of cold preservation with Collins' solution and received a similar intra-arterial dose plus a subcutaneous dose of EGF (0.5 ml. of 10(-3) M.) (N = 8) or vehicle alone (N = 6). Contralateral nephrectomy was performed in all animals. Daily creatinine measurements revealed no beneficial effect from EGF on recovery of renal function in Group 1 or 2 animals. Studies of EGF on pig proximal tubular cells demonstrated in vitro mitogenesis; autoradiography with 125I-EGF revealed binding of EGF throughout the kidney. Immunohistochemistry showed significant tubular cell proliferation in response to ischemic injury, without further enhancement from EGF. Thus, although exogenous EGF bound to pig kidney cells and stimulated cell proliferation, we were unable to demonstrate a clinically significant acceleration of recovery from ischemic injury.
Topics in top quark physics (1993)

The status of top quark searches will be briefly reviewed. Theoretical predictions for the top quark decay rate are presented including QCD and electroweak radiative corrections. The possibilities for quarkonium searches at an hadron collider will be discussed. The perspectives for top production at an electron positron collider will be described in detail with emphasis on the behavior of the cross section and decay distribution in the threshold region. 1 The ever-increasing energies of electron positron colliders from PETRA, PEP, and TRISTAN up to LEP as well as those of the hadron colliders Sp¯pS and TEVATRON have led to an impressive increase of the lower bound of the top quark mass. The limits from LEP (44.5 GeV) and from the absence of W → t + b as inferred from the W decay rate (54 GeV) are derived
Fourier Transform Near-Infrared Spectroscopy Application for Sea Salt Quality Evaluation (2011)

Near-infrared (NIR) spectroscopy in diffuse reflectance mode was explored with the objective of discriminating sea salts according to their quality type (traditional salt vs “flower of salt”) and geographical origin (Atlantic vs Mediterranean). Sea salts were also analyzed in terms of Ca2+, Mg2+, K+, alkalinity, and sulfate concentrations to support spectroscopic results. High concentrations of Mg2+ and K+ characterized Atlantic samples, while a high Ca2+ content was observed in traditional sea salts. A partial least-squares discriminant analysis model considering the 8500–7500 cm–1 region permitted the discrimination of salts by quality types. The regions 4650–4350 and 5900–5500 cm–1 allowed salts classification according to their geographical origin. It was possible to classify correctly 85.3 and 94.8% of the analyzed samples according to the salt type and to the geographical origin, respectively. These results demonstrated that NIR spectroscopy is a suitable and very efficient tool for sea salt quality evaluation.
Expression and characterization of recombinant vitamin K‐dependent γ‐glutamyl carboxylase from an invertebrate, Conus textile (2002)

The marine snail Conus is the sole invertebrate wherein both the vitamin K-dependent carboxylase and its product, gamma-carboxyglutamic acid, have been identified. To examine its biosynthesis of gamma-carboxyglutamic acid, we studied the carboxylase from Conus venom ducts. The carboxylase cDNA from Conus textile has an ORF that encodes a 811-amino-acid protein which exhibits sequence similarity to the vertebrate carboxylases, with 41% identity and approximately 60% sequence similarity to the bovine carboxylase. Expression of this cDNA in COS cells or insect cells yielded vitamin K-dependent carboxylase activity and vitamin K-dependent epoxidase activity. The recombinant carboxylase has a molecular mass of approximately 130 kDa. The recombinant Conus carboxylase carboxylated Phe-Leu-Glu-Glu-Leu and the 28-residue peptides based on residues -18 to +10 of human proprothrombin and proFactor IX with Km values of 420 micro m, 1.7 micro m and 6 micro m, respectively; the Km for vitamin K is 52 micro m. The Km values for peptides based on the sequence of the conotoxin epsilon-TxIX and two precursor analogs containing 12 or 29 amino acids of the propeptide region are 565 micro m, 75 micro m and 74 micro m, respectively. The recombinant Conus carboxylase, in the absence of endogenous substrates, is stimulated up to fivefold by vertebrate propeptides but not by Conus propeptides. These results suggest two propeptide-binding sites in the carboxylase, one that binds the Conus and vertebrate propeptides and is required for substrate binding, and the other that binds only the vertebrate propeptide and is required for enzyme stimulation. The marked functional and structural similarities between the Conus carboxylase and vertebrate vitamin K-dependent gamma-carboxylases argue for conservation of a vitamin K-dependent carboxylase across animal species and the importance of gamma-carboxyglutamic acid synthesis in diverse biological systems.
Dynamics and coherent control of high-amplitude optical phonons in bismuth (2001)

High-amplitude optical phonons in bismuth are generated through impulsive stimulated Raman scattering and detected through the induced change in the optical reflectivity. Reflectivity changes greater than 1% have been recorded. Phonon dynamics and coherent control in the high-amplitude regime are reported.
Reflective measurement of water concentration using millimeter wave illumination (2011)

THz and millimeter wave technology have shown the potential to become a valuable medical imaging tool because of its sensitivity to water and safe, non-ionizing photon energy. Using the high dielectric constant of water in these frequency bands, reflectionmode THz sensing systems can be employed to measure water content in a target with high sensitivity. This phenomenology may lead to the development of clinical systems to measure the hydration state of biological targets. Such measurements may be useful in fast and convenient diagnosis of conditions whose symptoms can be characterized by changes in water concentration such as skin burns, dehydration, or chemical exposure. To explore millimeter wave sensitivity to hydration, a reflectometry system is constructed to make water concentration measurements at 100 GHz, and the minimum detectable water concentration difference is measured. This system employs a 100 GHz Gunn diode source and Golay cell detector to perform point reflectivity measurements of a wetted polypropylene towel as it dries on a mass balance. A noise limited, minimum detectable concentration difference of less than 0.5% by mass can be detected in water concentrations ranging from 70% to 80%. This sensitivity is sufficient to detect hydration changes caused by many diseases and pathologies and may be useful in the future as a diagnostic tool for the assessment of burns and other surface pathologies.
Maize Bran Particle Size Governs the Community Composition and Metabolic Output of Human Gut Microbiota in in vitro Fermentations (2020)

Differences in the chemical and physical properties of dietary fibers are increasingly known to exert effects on their fermentation by gut microbiota. Here, we demonstrate that maize bran particle size fractions show metabolic output and microbial community differences similar to those we previously observed for wheat brans. As for wheat brans, maize bran particles varied in starch and protein content and in sugar composition with respect to size. We fermented maize bran particles varying in size <i>in vitro</i> with human fecal microbiota as inocula, measuring their metabolic fate [i.e., short-chain fatty acids (SCFAs)] and resulting community structure (via 16S rRNA gene amplicon sequencing). Metabolically, acetate, propionate and butyrate productions were size-dependent. 16S rRNA sequencing revealed that the size-dependent SCFA production was linked to divergent microbial community structures, which exerted effects at fine taxonomic resolution (the genus and species level). These results further suggest that the physical properties of bran particles, such as size, are important variables governing microbial community compositional and metabolic responses.
Osteoprotegerin Is an αvβ3-induced, NF-κB-dependent Survival Factor for Endothelial Cells (2000)

Osteopontin protects endothelial cells from apoptosis induced by growth factor withdrawal. This interaction is mediated by the alpha(v)beta(3) integrin and is NF-kappaB-dependent (Scatena, M., Almeida, M., Chaisson, M. L., Fausto, N., Nicosia, R. F., and Giachelli, C. M. (1998) J. Cell Biol. 141, 1083-1093). In the present study we used differential cloning to identify osteopontin-induced, NF-kappaB-dependent genes in endothelial cells. One of the genes identified in this screen was osteoprotegerin, a member of the tumor necrosis factor receptor superfamily. By Northern and Western blot analysis, osteoprotegerin mRNA and protein levels were very low in endothelial cells plated on the non-integrin cell attachment factor, poly-d-lysine. In contrast, osteoprotegerin mRNA and protein levels were induced 5-7-fold following alpha(v)beta(3) ligation by osteopontin. Osteoprotegerin induction by osteopontin was time-dependent and observed as early as 3 h following treatment. NF-kappaB inactivation achieved by over expression of an IkappaB super repressor in endothelial cells completely inhibited osteoprotegerin induction by osteopontin. Finally, purified osteoprotegerin protected endothelial cells with inactive NF-kappaB from apoptosis induced by growth factor deprivation. These data suggest that alpha(v)beta(3)-mediated endothelial survival depends on osteoprotegerin induction by NF-kappaB and indicate a new function for osteoprotegerin in endothelial cells.
Axe looms for European research body (2014)

The European Science Foundation could be closed by the end of the year as many of its members look to Brussels. Edwin Cartlidge reports.
Structural Studies on the Effects of ZrO[sub 2] Coating on LiCoO[sub 2] during Cycling Using In Situ X-Ray Diffraction Technique (2006)

The effects of -coating on the surface of have been studied using synchrotron-based in situ x-ray diffraction (XRD) technique. Although both -coated and uncoated showed capacity fading during high voltage cycling, the coated one showed better cycle performance. After observing capacity fade for both samples through 10 charge-discharge cycles, in situ XRD patterns were collected during the 11th charge with reduced current density. With reduced current density, both samples restored part of their lost capacity. However, in situ XRD data shows that the -coated sample has much better structural change behaviors than the uncoated . The partial restoration of the lost capacity and the recovered structural variations observed at reduced current density clearly indicates that the lost capacity is very closely related to the increased polarization, which is most likely due to the precipitation of the electrolyte decomposition products on the surface of cathode material. coating layer may provide some protection for the cathode surface and help to reduce the electrolyte decomposition at higher voltages.
Vaccination Strategy Determines the Emergence and Dominance of CD8+ T-Cell Epitopes in a FVB/N Rat HER-2/neuMouse Model of Breast Cancer (2006)

The HER-2/neu oncogene has >25 HLA epitopes, yet only one FVB/N mouse CD8(+) T-cell epitope has been mapped to date. This epitope has been termed the immunodominant epitope for the FVB/N mouse, but we propose that the vaccination strategy determines the dominance of epitopes. Using a series of overlapping peptides, we have mapped another CD8(+) T-cell epitope that emerges in the FVB/N mouse following vaccination with Listeria monocytogenes-based vaccines that express fragments of HER-2/neu. Following the identification of this novel H-2K(q)-restricted epitope, we sought to compare the T-cell response to this epitope with the previously identified PDSLRDLSVF epitope. This newly identified epitope and the previously identified epitope lie within fragments contained in different vaccines, the PDSLRDLSVF epitope in Lm-LLO-EC2 and the newly identified PYNYLSTEV epitope in Lm-LLO-EC1; thus, it has been possible to compare the responses of these epitopes independent of any competing response between the epitopes. CTL analysis of individual peptide-pulsed target cells and intracellular cytokine stain for IFN-gamma produced by splenocytes from Lm-LLO-EC1 compared with Lm-LLO-EC2 vaccinated FVB/N mice shows that there is no difference between the responses generated to either of these epitopes. We also show that the avidity of the CD8(+) T cells for either of these epitopes is similar based on the concentration of peptide necessary to mediate similar levels of lysis of target cells. In addition, HER-2/neu DNA vaccination followed by CTL analysis further showed that both of these peptides can emerge as epitopes.
Human-Based Human Milk Fortifier as Rescue Therapy in Very Low Birth Weight Infants Demonstrating Intolerance to Bovine-Based Human Milk Fortifier (2017)

Very low birth weight and preterm infants with GI intolerance to BHMF were successfully rescued with use of HMHMF. Improvements in growth were achieved without need for supplementation with PN through achievement of sufficient enteral calorie and protein intakes.
Toward multi-stage decoupled visual SLAM system (2013)

SLAM is defined as simultaneous estimation of mobile robot pose and structure of the surrounding environment Currently, there is a much interest in Visual SLAM, SLAM with a camera as main sensor, because the camera is an ubiquitous and affordable sensor. Camera measurements formed by perspective projection is highly nonlinear with respect to estimated states, leading to complicated nonlinear estimation problem. In this paper, a novel system is proposed that divides the problem into two parts: local and global motion estimation. This division leads to a simple linear estimation system. In the first stage, local motion parameters (acceleration, velocity, angular acceleration and orientation) are estimated in robot local frame. Robot position and the scene map are then estimated in the second stage in global frame as global motion parameters. Map is updated at each camera frame and is represented in a relative way to decouple robot pose from map structure estimation. The new system simplified the map correction to a linear optimization problem. Simulation results showed that the proposed system converges and yields accurate results.
Isolation and characterization of a regulatory gene affecting rhamnolipid biosurfactant synthesis in Pseudomonas aeruginosa (1994)

A mutant strain (65E12) of Pseudomonas aeruginosa that is unable to produce rhamnolipid biosurfactants and lacks rhamnosyltransferase activity was genetically complemented by using a P. aeruginosa PG201 wild-type gene library. A single complementing cosmid was isolated on the basis of surface tension measurements of subcultures of the transconjugants by using a sib selection strategy. The subcloning of the complementing cosmid clone yielded a 2-kb fragment capable of restoring rhamnolipid biosynthesis, rhamnosyltransferase activity, and utilization of hexadecane as a C source in mutant 65E12. The nucleotide sequence of the complementing 2-kb fragment was determined, and a single open reading frame (rhlR) of 723 bp specifying a putative 28-kDa protein (RhlR) was identified. Sequence homologies between the RhlR protein and some regulatory proteins such as LasR of P. aeruginosa, LuxR of Vibrio fischeri, RhiR of Rhizobium leguminosarum, and the putative activator 28-kDa UvrC of Escherichia coli suggest that the RhlR protein is a transcriptional activator. A putative target promoter which is regulated by the RhlR protein has been identified 2.5 kb upstream of the rhlR gene. Multiple plasmid-based rhlR gene copies had a stimulating effect on the growth of the P. aeruginosa wild-type strain in hexadecane-containing minimal medium, on rhamnolipid production, and on the production of pyocyanin chromophores. Disruption of the P. aeruginosa wild-type rhlR locus led to rhamnolipid-deficient mutant strains, thus confirming directly that this gene is necessary for rhamnolipid biosynthesis. Additionally, such PG201::'rhlR' mutant strains lacked elastase activity, indicating that the RhlR protein is a pleiotropic regulator.
Protease sensing with nanoparticle based platforms (2010)

Nanoparticulate systems in various unique configurations are highly effective at detecting protease activity both in vivo and in vitro. In this article, we have summarised the conventional modern methods for monitoring protease activity, and critically appraised recent advances in protease-responsive nanosensors.
Crystallization of PNMT, the adrenaline-synthesizing enzyme, is critically dependent on a high protein concentration (2002)

Phenylethanolamine N-methyltransferase, PNMT, utilizes the methylating cofactor S-adenosyl-L-methionine to catalyse the synthesis of adrenaline. Human PNMT has been crystallized in complex with an inhibitor and the cofactor product S-adenosyl-L-homocysteine using the hanging-drop technique with PEG 6000 and lithium chloride as precipitant. A critical requirement for crystallization was a high enzyme concentration (>90 mg ml(-1)) and cryocrystallography was used for high-quality data measurement. Diffraction data measured from a cryocooled crystal extend to a resolution of 2.3 A. Cryocooled crystals belong to space group P4(3)2(1)2 and have unit-cell parameters a = b = 94.3, c = 187.7 A.
Oligodendrocyte precursors originate at the ventral ventricular zone dorsal to the ventral midline region in the embryonic rat spinal cord (1993)

The precursors for oligodendrocytes, the myelinating cells of the vertebrate CNS, appear to be initially restricted to ventral regions of the embryonic rat spinal cord. These cells subsequently populate dorsal spinal cord regions where they acquire the mature characteristics of oligodendrocytes. To determine the location and timing of proliferation of oligodendrocyte precursors in the ventral spinal cord, and to map their pathways of migration in vivo, an assay that identifies mitotic cells was used in conjunction with antibodies that distinguish astrocytes, oligodendrocytes and their precursors. Between E16.5 and E18.5, two hours after a maternal injection of BrdU, the majority of proliferating cells were located in a discrete cluster at the ventral ventricular zone dorsal to the ventral midline region of the developing spinal cord. By contrast, 12-24 hours following a BrdU injection at E16.5, increasing numbers of labeled cells were seen in the dorsal and more lateral locations of the spinal cord. These observations suggest that BrdU-labeled ventral ventricular cells, or their progeny migrate dorsally and laterally during subsequent spinal cord development. To determine the nature of these proliferating cells, cultures of dorsal and ventral spinal cord from BrdU-labeled animals were double-labeled with antibodies that identify oligodendrocytes or astrocytes and anti-BrdU. In dorsal spinal cord cultures derived from animals that had received a single injection of BrdU at E16.5, the majority of proliferating cells differentiated into astrocytes while, in ventrally derived cultures from the same animals, the majority of proliferating cells differentiated into oligodendrocytes. In dorsal cultures prepared from animals that received multiple injections of BrdU between E16.5 and E18.5, many more cells were labeled with BrdU and approximately half of these differentiated into oligodendrocytes. These observations suggest that during embryonic development proliferating oligodendrocyte precursors are initially located at the ventral ventricular zone dorsal to the ventral midline region of the spinal cord and during subsequent maturation these cells or their progeny migrated dorsally in the ventricular region of the spinal cord, and laterally to reside in the developing white matter.
Brain nuclear magnetic resonance imaging enhanced by a paramagnetic nitroxide contrast agent: preliminary report (1983)

Contrast-enhancing agents for demonstrating abnormalities of the blood-brain barrier may extend the diagnostic utility of proton nuclear magnetic resonance (NMR) imaging. "TES," a nitroxide stable free radical derivative, was tested as a central nervous system contrast enhancer in dogs with experimentally induced unilateral cerebritis or radiation cerebral damage. After intravenous injection of TES, the normal brain showed no change in NMR appearance, but areas of disease demonstrated a dramatic increase (up to 45%) in spin-echo intensity and a decrease in T1 relaxation times. The areas of disease defined by TES enhancement were either not evident on the nonenhanced NMR images or were better defined after contrast administration. In-depth tests of toxicity, stability, and metabolism of this promising NMR contrast agent are now in progress.
R/qtl: QTL mapping in experimental crosses (2003)

The package is freely available at http://www.biostat.jhsph.edu/~kbroman/qtl.
Statistical profile estimation in database systems (1988)

A statistical profile summarizes the instances of a database. It describes aspects such as the number of tuples, the number of values, the distribution of values, the correlation between value sets, and the distribution of tuples among secondary storage units. Estimation of database profiles is critical in the problems of query optimization, physical database design, and database performance prediction. This paper describes a model of a database of profile, relates this model to estimating the cost of database operations, and surveys methods of estimating profiles. The operators and objects in the model include build profile, estimate profile, and update profile. The estimate operator is classified by the relational algebra operator (select, project, join), the property to be estimated (cardinality, distribution of values, and other parameters), and the underlying method (parametric, nonparametric, and ad-hoc). The accuracy, overhead, and assumptions of methods are discussed in detail. Relevant research in both the database and the statistics disciplines is incorporated in the detailed discussion.