gebhart/patrepeval huggingface dataset:
Alterations in cellular calcium and magnesium during circulatory/septic shock. (1989)

Hepatic cellular and mitochondrial Ca2+ and Mg2+ contents and the role of these ions in cellular dysfunction were studied in rat hemorrhagic and endotoxic models which simulate various facets of human circulatory/septic shock states. Hemorrhagic shock was induced by bleeding rats to a state of vascular decompensation at the mean arterial pressure of 40 mm Hg. Endodotoxic shock was ascertained after observing hypoglycemia, hyperlacticacidemia and hemorrhagic bowel lesions in rats injected with Salmonella enteritidis endotoxin (15-20 mg/kg). In a late stage of hemorrhagic shock, significant changes occurred in mitochondrial ion contents; Ca2+ increased and Mg2+ decreased as compared to controls. These ionic changes were correlated with depressed mitochondrial respiratory functions. Addition of 6 mM Mg2+ to shocked-rat isolated mitochondria significantly restored mitochondrial functions. In endotoxic shock, hepatic Mg2+ content was significantly lower compared to controls. Treatment of rats with the calcium antagonist, diltiazem, several minutes prior to endotoxin injections, resulted in restoration of hepatic cellular Mg2+ to control levels. Studies of hepatic intracellular Ca2+ regulation in endotoxic shock revealed (1) an elevation in free cytosolic Ca2+, (2) a blunting of catecholamine-mediated increase in cytosolic Ca2+ and (3) an inhibition of intracellular messenger-induced Ca2+ release by the endoplasmic reticulum.
Biosynthesis of marine natural products: microorganisms (Part A) (2005)

Covering: 1999 through 2004. Previous review: Nat. Prod. Rep., 1999, 16, 653
Potential role of Demodex mites and bacteria in the induction of rosacea (2012)

Rosacea is a common dermatological condition that predominantly affects the central regions of the face. Rosacea affects up to 3 % of the world's population and a number of subtypes are recognized. Rosacea can be treated with a variety of antibiotics (e.g. tetracycline or metronidazole) yet no role for bacteria or microbes in its aetiology has been conclusively established. The density of Demodex mites in the skin of rosacea patients is higher than in controls, suggesting a possible role for these mites in the induction of this condition. In addition, Bacillus oleronius, known to be sensitive to the antibiotics used to treat rosacea, has been isolated from a Demodex mite from a patient with papulopustular rosacea and a potential role for this bacterium in the induction of rosacea has been proposed. Staphylococcus epidermidis has been isolated predominantly from the pustules of rosacea patients but not from unaffected skin and may be transported around the face by Demodex mites. These findings raise the possibility that rosacea is fundamentally a bacterial disease resulting from the over-proliferation of Demodex mites living in skin damaged as a result of adverse weathering, age or the production of sebum with an altered fatty acid content. This review surveys the literature relating to the role of Demodex mites and their associated bacteria in the induction and persistence of rosacea and highlights possible therapeutic options.
Experimental demonstration of dual recycling for interferometric gravitational-wave detectors (1991)

We describe the first experimental demonstration of dual recycling, an optical system which should improve considerably the performance of proposed laser-interferometric gravitational-wave detectors. The results were in excellent agreement with predictions: An enhancement of the signal-to-noise ratio by a factor of 7 was observed.
Holographic recording of fast events on a CCD camera (2002)

We report on holographic recording of nanosecond events on a conventional CCD camera. Three frames of an air-discharge event, with resolution of 5.9 ns and frame interval of 12 ns, are recorded in a single CCD frame. Each individual frame is reconstructed by digital filtering of the CCD frame, since successively recorded holograms are centered at different carrier frequencies in the spatial frequency domain.
Well-defined NHC-rhodium hydroxide complexes as alkenehydrosilylation and dehydrogenative silylation catalysts (2012)

Alkene hydrosilylation and dehydrogenative silylation reactions, mediated by [Rh(cod)(NHC)(OH)] complexes (cod = 1,5-cyclooctadiene; NHC = N-heterocyclic carbene) are described. The study details a comparison of the catalytic activity and steric characteristics of four rhodium complexes bearing different NHC ligands. The novel [Rh(cod)(Ii-PrMe)(OH)] complex (Ii-PrMe = 1,3-diisopropyl-4,5-dimethylimidazol-2-ylidine) was designed to improve the reactivity of Rh(I)-hydroxides and proved to be a successful promoter of hydrosilylation and dehydrogenative silylation, displaying good stereo- and regiocontrol.
A target for carbon source-dependent negative regulation of the citB promoter of Bacillus subtilis (1990)

Expression of the aconitase (citB) gene of Bacillus subtilis is subject to catabolite repression in cells grown in minimal media. In nutrient broth medium, citB expression is low in growing cells but is induced when cells enter sporulation. A 600-base-pair DNA fragment that extends from positions -400 through +200, relative to the transcription start site, was shown to include all of the cis-acting sequences necessary for catabolite repression and sporulation-associated regulation. This was demonstrated by fusing this DNA fragment to the Escherichia coli lacZ gene, integrating the fusion in the amyE locus of the B. subtilis chromosome, and measuring the regulation of expression of beta-galactosidase. By creating a series of deletions from either end of the 600-base-pair fragment, it was possible to define a target for catabolite repression; at least part of this target lies within the sequence between positions -84 and -68. DNA fragments that included positions -84 through +36, when carried on high-copy plasmids, caused derepression of aconitase synthesis, as if a negative regulator were being titrated. The same plasmids caused derepression of citrate synthase activity as well. Deletion of the sequence between positions -84 and -67 abolished this titration effect for both enzymes. Mutations that altered the target for catabolite repression also affected the inducibility of citB at the onset of sporulation, at least when sporulation was induced by the addition of decoyinine, an inhibitor of guanine nucleotide synthesis. When sporulation was induced by exhaustion of nutrient broth, there was no detectable difference in expression of citB-lacZ fusions whether or not they had the citB sequence from positions -84 to -67, suggesting that the mechanisms of regulation of citB in minimal medium and nutrient broth are different.
Publisher’s Note: Kaon Condensation, Black Holes, and Cosmological Natural Selection [Phys. Rev. Lett.101, 091101 (2008)] (2008)

Received 2 September 2008DOI:https://doi.org/10.1103/PhysRevLett.101.119901©2008 American Physical Society
An introduction to quadrupole–time‐of‐flight mass spectrometry (2001)

A brief introduction is presented to the basic principles and application of a quadrupole-time-of-flight (TOF) tandem mass spectrometer. The main features of reflecting TOF instruments with orthogonal injection of ions are discussed. Their operation and performance are compared with those of triple quadrupoles with electrospray ionization and matrix-assisted laser desorption/ionization (MALDI) TOF mass spectrometers. Examples and recommendations are provided for all major operational modes: mass spectrometry (MS) and tandem MS (MS/MS), precursor ion scans and studies of non-covalent complexes. Basic algorithms for liquid chromatography/MS/MS automation are discussed and illustrated by two applications.
The Solid State (1997)

This chapter contains sections titled: Introduction Bonds in Solids Details of the Model Bands in Solids Insulators and Semiconductors Some Properties of Metals Clusters and Surfaces Recent Applications of Concepts References
Coupling backbone flexibility and amino acid sequence selection in protein design (1997)

Using a protein design algorithm that considers side-chain packing quantitatively, the effect of explicit backbone motion on the selection of amino acids in protein design was assessed in the core of the streptococcal protein G beta 1 domain (G beta 1). Concerted backbone motion was introduced by varying G beta 1's supersecondary structure parameter values. The stability and structural flexibility of seven of the redesigned proteins were determined experimentally and showed that core variants containing as many as 6 of 10 possible mutations retain native-like properties. This result demonstrates that backbone flexibility can be combined explicitly with amino acid side-chain selection and that the selection algorithm is sufficiently robust to tolerate perturbations as large as 15% of G beta 1's native supersecondary structure parameter values.
Microplastic Structures (1986)

Thick coatings (5-15&mu;m) of a new dual image, aqueous developable photoresist can be exposed using a light attenuating photomask consisting of clear, opaque and grey areas and then processed to yield thermally stable 3-dimensional structures which are potentially useful as mechanical and optical components of devices. In the positive mode, relief and intaglio images are produced by processing similar to positive novolak based resists with 1- 2&mu;m resolution and with the added feature that the images can be made thermally stable to temperatures &gt;300° C. Negative mode processing of coated wafers imaged with the special mask produces thermally stable structures with tunnels or hollow chambers as well as cantilever beams. Because these structures are crosslinked at the time of development, processing in the negative mode shows much wider latitude than is the case in the positive mode. Images by negative mode processing are capable of submicron resolution, higher aspect ratio (&gt;3 vs &lt;1.6), and inward sloping wall profiles adjustable by exposure. The acid hardening resin compositions cover a broad range of compositions so that resins can be tailored to meet specific property requirements.
Exploring sketch beautification techniques (2005)

Beautification of vague, imprecise sketchy ink input is an interesting area for exploration, especially with the emergence of pen-based systems, such as the Tablet PC. Fifty percent of the total time spent creating drawings on a computer is on formalisation operations [3], why waste this time when the same result is achievable via recognition and beautification techniques? We examined beautification and its value in supporting the design process by prototyping a design tool incorporating several beautification techniques. The following is a description of the design, construction and evaluation of our grid based design environment.
Spread spectrum mobile radio, 1977-1982 (1983)

In 1977, Cooper and Nettleton proposed a spread spectrum mobile radio system using frequency-hopping multiple access, Hadamard coding for error correction, and differential phase shift keyed (DPSK) modulation, and they claimed higher spectral efficiency than frequency-division (FD) FM systems. Subsequent analyses showed that the DPSK system has a spectral efficiency of 8.4 percent as compared to the efficiency of unity for a FD-FM system with 30-kHz channel spacings. Goodman et al. suggested an alternative modulation scheme in 1980, using multilevel frequency shift keying (MFSK), and a 30 percent efficiency was obtained. The research results in spread spectrum mobile radio are summarized, and the areas requiring further investigation before a commercial system can be implemented are identified.
Deeply etched MMI-based components on 4 μm thick SOI for SOA-based optical RAM cell circuits (2013)

We present novel deeply etched functional components, fabricated by multi-step patterning in the frame of our 4 &mu;m thick Silicon on Insulator (SOI) platform based on singlemode rib-waveguides and on the previously developed rib-tostrip converter. These novel components include Multi-Mode Interference (MMI) splitters with any desired splitting ratio, wavelength sensitive 50/50 splitters with pre-filtering capability, multi-stage Mach-Zehnder Interferometer (MZI) filters for suppression of Amplified Spontaneous Emission (ASE), and MMI resonator filters. These novel building blocks enable functionalities otherwise not achievable on our SOI platform, and make it possible to integrate optical RAM cell layouts, by resorting to our technology for hybrid integration of Semiconductor Optical Amplifiers (SOAs). Typical SOA-based RAM cell layouts require generic splitting ratios, which are not readily achievable by a single MMI splitter. We present here a novel solution to this problem, which is very compact and versatile and suits perfectly our technology. Another useful functional element when using SOAs is the pass-band filter to suppress ASE. We pursued two complimentary approaches: a suitable interleaved cascaded MZI filter, based on a novel suitably designed MMI coupler with pre-filtering capabilities, and a completely novel MMI resonator concept, to achieve larger free spectral ranges and narrower pass-band response. Simulation and design principles are presented and compared to preliminary experimental functional results, together with scaling rules and predictions of achievable RAM cell densities. When combined with our newly developed ultra-small light-turning concept, these new components are expected to pave the way for high integration density of RAM cells.
Improving outcomes of cord blood transplantation: HLA matching, cell dose and other graft‐ and transplantation‐related factors (2009)

The use of unrelated umbilical cord blood (UCB) as an alternative source of haematopoietic stem cells transplantation (HSCT) has been widely used for patients lacking a human leucocyte antigen (HLA) matched donor. One of the disadvantages of using UCB is the limited number of haematopoietic stem cells and, consequently, delayed engraftment and increased risk of early mortality. Many approaches have been investigated in the attempt to improve engraftment and survival. Among those, studies analysing prognostic factors related to patients, disease, donor and transplantation have been performed. Variable factors have been identified, such as factors related to donor choice (HLA, cell dose and others) and transplantation (conditioning and graft-versus-host disease prophylaxis regimens). This review will focus on the interactions between HLA, cell dose and other modifiable factors related to the UCB unit selection and transplantation that may improve outcomes after UCB transplantation.
Optimum Rebalancing of the 3-Hydroxypropionic Acid Production Pathway from Glycerol in Escherichia coli (2016)

3-Hydroxypropionic acid (3-HP) can be biologically produced from glycerol by two consecutive enzymatic reactions, dehydration of glycerol to 3-hydroxypropionaldehyde (3-HPA) and oxidation of 3-HPA. The pathway has been proved efficient, but imbalance between the rates of the two enzymatic reactions often results in the accumulation of the toxic 3-HPA, which severely reduces cell viability and 3-HP production. In this study, we used UTR engineering to maximally increase the activities of glycerol dehydratase (GDHt) and aldehyde dehydrogenase (ALDH) for the high conversion of glycerol to 3-HP. Thereafter, the activity of GDHt was precisely controlled to avoid the accumulation of 3-HPA by varying expression of dhaB1, a gene encoding a main subunit of GDHt. The optimally balanced E. coli HGL_DBK4 showed a substantially enhanced 3-HP titer and productivity compared with the parental strain. The yield on glycerol, 0.97 g 3-HP/g glycerol, in a fed-batch experiment, was the highest ever reported.
Nonswellable and swellable ethylene glycol dimethacrylate-acrylic acid copolymer microspheres (1996)

In this study, nonswellable and swellable poly(ethylene glycol dimethacrylate/acrylic acid) copolymer microspheres, in the size range of 50–150 μm, were produced by conventional and modified suspension copolymerizations of the respective monomers, i.e., ethyleneglycol dimethacrylate (EGDMA) and acrylic acid (AA) in aqueous media. Poly(vinyl alcohol) and benzoyl peroxide were used as the stabilizer and the initiator. The diluent, i.e., toluene was included in the polymerization recipe of the modified suspension polymerization. The microspheres were characterized by optical microscopy, FTIR, and FTIR-DRS, and potentiometric titrations. Highly crosslinked, transparent, and nonswellable poly(EGDMA/AA) microspheres were obtained with the conventional suspension polymerization procedure. The modified suspension polymerization provided swellable, opaque, and crosslinked copolymer microspheres. Acrylic acid incorporation into the copolymeric microspheres were significantly higher in the modified procedure, relative to the conventional procedure. © 1996 John Wiley & Sons, Inc.
Role of epidermal growth factor receptor family members in growth and differentiation of breast carcinoma. (1998)

Members of the epidermal growth factor (EGF) family of tyrosine kinase receptors are involved in the regulation of cell growth and differentiation, and are found to be expressed in many types of cancers. Activation of these receptors can be elicited by multiple ligands, resulting in the formation of a spectrum of heterodimer complexes and a number of biological outcomes. A clear demonstration of biological activation by a single complex has been difficult to address because of the endogenous expression of HERs (human EGF-like receptors) in many cell lines. We have generated a collection of cell lines expressing all HERs alone or in all pairwise combinations in a clone of NIH 3T3 cells (3T3-7d) devoid of detectable EGF receptor family members. Transformation, as measured by growth in soft agar, only occurred in cells expressing two different HER family members. Transformation with activated Neu and the rate of in vivo tumour formation were also correlated with the expression of multiple HERs in the same cell. To further our understanding of the role of heterodimer signalling, we demonstrated that, within a breast carcinoma cell line, activation of HER-3 results in cellular differentiation, prolonged activation of extracellular-signal-related kinase 1 (ERK1) activity and an increase in p21CIP1/WAF1 nuclear staining. In contrast, activation of HER-4 is mitogenic, induces transient activation of ERK1 activity and decreases the nuclear staining of p21CIP1/WAF1. These differences in biochemical and biological responses are correlated with the contrasting abilities of HER-3 and HER-4 to be down-regulated from the cell surface. The cell-surface localization of HER-3 does not change in response to ligand, whereas activation of HER-4 results in a loss of cell-surface staining followed by accumulation into a perinuclear compartment.
What is the real role of antimicrobial polypeptides that can mediate several other inflammatory responses? (2003)

Antimicrobial peptides are effector molecules of innate immunity with microbicidal and pro- or anti-inflammatory activities. Their role is now widening following evidence that one such multifunctional peptide, LL-37, induces angiogenesis, a process essential for host defense, wound healing, and tissue repair.
Binding of Neomycin to the TAR Element of HIV-1 RNA Induces Dissociation of Tat Protein by an Allosteric Mechanism (1998)

Neomycin inhibits the binding of Tat-derived peptides to the trans-activating region (TAR) of HIV-1 RNA. Kinetic studies reveal that neomycin acts as a noncompetitive inhibitor that can bind to the Tat-TAR complex and increase the rate constant (koff) for dissociation of the peptide from the RNA. Neomycin effects a conformational change in the structure of TAR that can be detected by circular dichroism spectroscopy. The increase in ellipticity measured at 265 nm upon binding of the aminoglycoside is opposite to the decrease seen when Tat peptides bind to the RNA. Thus, the structural transition induced by neomycin is apparently incompatible with the binding of Tat and underlies the inhibitory action of the antibiotic. The binding site for neomycin on TAR was identified in ribonuclease protection experiments and is located in the stem immediately below the three-nucleotide bulge that serves as the primary identity element for Tat. Apparent protection of residues in the bulge by neomycin may represent additional contacts to the aminoglycoside, but more likely result from changes in the structure of this region when the ligand binds to the RNA. Binding assays using variants of TAR in which inosine residues were substituted for guanosine residues support the results from the ribonuclease protection experiments. Inosine substitutions in the lower stem, but not the upper stem, decrease the binding constant for neomycin by approximately 100-fold. Neither of these variants affected the binding affinity of Tat peptide. In addition, these latter experiments suggest that the aminoglycoside may be located in the minor groove of the stem. This mode of association may be a critical aspect of neomycin's ability to bind to the Tat-TAR complex and could serve as a guide for the design of other drugs that bind to specific RNA targets as noncompetitive inhibitors.
Facile Epoxidation Strategy for Producing Amphiphilic Up-Converting Rare-Earth Nanophosphors as Biological Labels (2008)

The biological application of up-converting rare-earth nanophosphors (UCNPs) is still restricted because of unfavorable surface properties. Herein, the development of a simple, effective, and versatile method for converting hydrophobic UCNPs into amphiphilic ones, based on epoxidation of the surface oleic acid (OA) ligand and further coupling with polyethylene glycol monomethyl ether (mPEG-OH), is described. The successful epoxidation and effective coating of the surface of the UCNPs by mPEG-OH have been confirmed by 1H NMR spectrometry, Fourier-transform infrared (FTIR) spectroscopy, and dynamic light scattering (DLS) studies. Investigations by transmission electron microscopy (TEM) and photoluminescence (PL) spectroscopy showed no obvious variations in the morphologies and luminescent properties of the UCNPs during the epoxidation and functionalization processes. In particular, the low cytotoxicity and good cell membrane permeability of the resulting amphiphilic mPEG-UCNPs make them promising candidates for use as bioimaging probes.
Influence of Immunogenicity on the Long-Term Efficacy of Infliximab in Crohn's Disease (2003)

The development of antibodies against infliximab is associated with an increased risk of infusion reactions and a reduced duration of response to treatment. Concomitant immunosuppressive therapy reduces the magnitude of the immunogenic response.
RSA 2004: Combined Basic Research Satellite Symposium - Session Three: Alcohol and Mitochondrial Metabolism: At the Crossroads of Life and Death (2005)

This article summarizes the proceedings of the RSA 2004 Combined Basic Research Satellite Meeting convened at the Westin Bayshore Resort and Marina, Vancouver, CA. One of the sessions "Alcohol and mitochondrial metabolism: At the crossroads of life and death" featured five speakers and was chaired by Drs. Jan Hoek and Sam Zakhari. The presentations were 1) INTRODUCTION: Alcohol and cellular energy metabolism by Jan Hoek, 2) Ethanol-dependent dysfunction of mitochondrial energy metabolism: the role of NO by Victor Darley-Usmar, 3) Ethanol and apoptosis in the heart by Gyorgy Hajnoczky, 4) Alcohol and mitochondrial biogenesis in development by Thomas Knudsen, and 5) Alcohol, mitochondrial function and cardiac preconditioning by Daria Mochly-Rosen.