gebhart/patrepeval huggingface dataset:
CO AS A CELLULAR SIGNALING MOLECULE (2005)

Many biological functions of heme oxygenase (HO), such as cytoprotection against oxidative stress, vasodilation, neurotransmission in the central or peripheral nervous systems, and anti-inflammatory, anti-apoptotic, or anti-proliferative potential, have been attributed to its enzymatic byproduct carbon monoxide (CO), although roles for biliverdin/bilirubin and iron have also been proposed. In addition to these well-characterized effects, recent findings reveal that HO-derived CO may act as an oxygen sensor and circadian modulator of heme biosynthesis. In lymphocytes, CO may participate in regulatory T cell function. A number of the known signaling effects of CO depend on stimulation of soluble guanylate cyclase and/or activation of mitogen-activated protein kinases (MAPK). Furthermore, modulation of caveolin-1 status may serve as an essential component of certain aspects of CO action, such as growth control. In this review, we summarize recent findings of the beneficial or detrimental effects of endogenous CO with an emphasis on the signaling pathways and downstream targets that trigger the action of this gas.
Matrix Metalloproteinase Expression Increases After Cerebral Focal Ischemia in Rats (1998)

These results demonstrate that early increased MMP-9 expression in endothelial cells and infiltrating neutrophils is a significant response to cerebral focal ischemia and that selective inhibition of MMP-9 activity can significantly reduce brain injury after stroke.
Differential Requirements for Tumor Necrosis Factor Receptor-associated Factor Family Proteins in CD40-mediated Induction of NF-κB and Jun N-terminal Kinase Activation (1999)

CD40 is a member of the tumor necrosis factor receptor family that mediates a number of important signaling events in B-lymphocytes and some other types of cells through interaction of its cytoplasmic (ct) domain with tumor necrosis factor receptor-associated factor (TRAF) proteins. Alanine substitution and truncation mutants of the human CD40ct domain were generated, revealing residues critical for binding TRAF2, TRAF3, or both of these proteins. In contrast to TRAF2 and TRAF3, direct binding of TRAF1, TRAF4, TRAF5, or TRAF6 to CD40 was not detected. However, TRAF5 could be recruited to wild-type CD40 in a TRAF3-dependent manner but not to a CD40 mutant (Q263A) that selectively fails to bind TRAF3. CD40 mutants with impaired binding to TRAF2, TRAF3, or both of these proteins completely retained the ability to activate NF-kappaB and Jun N-terminal kinase (JNK), implying that CD40 can stimulate TRAF2- and TRAF3-independent pathways for NF-kappaB and JNK activation. A carboxyl-truncation mutant of CD40 lacking the last 32 amino acids required for TRAF2 and TRAF3 binding, CD40(Delta32), mediated NF-kappaB induction through a mechanism that was suppressible by co-expression of TRAF6(DeltaN), a dominant-negative version of TRAF6, but not by TRAF2(DeltaN), implying that while TRAF6 does not directly bind CD40, it can participate in CD40 signaling. In contrast, TRAF6(DeltaN) did not impair JNK activation by CD40(Delta32). Taken together, these findings reveal redundancy in the involvement of TRAF family proteins in CD40-mediated NF-kappaB induction and suggest that the membrane-proximal region of CD40 may stimulate the JNK pathway through a TRAF-independent mechanism.
Mammographic Density as a Surrogate Marker for the Effects of Hormone Therapy on Risk of Breast Cancer (2006)

Although the effects of hormone therapy on mammographic density were greater in cases than controls, we did not find evidence that these effects were causally related to risk of breast cancer.
Semi-supervised learning using Gaussian fields and harmonic functions (2003)

An approach to semi-supervised learning is proposed that is based on a Gaussian random field model. Labeled and unlabeled data are represented as vertices in a weighted graph, with edge weights encoding the similarity between instances. The learning problem is then formulated in terms of a Gaussian random field on this graph, where the mean of the field is characterized in terms of harmonic functions, and is efficiently obtained using matrix methods or belief propagation. The resulting learning algorithms have intimate connections with random walks, electric networks, and spectral graph theory. We discuss methods to incorporate class priors and the predictions of classifiers obtained by supervised learning. We also propose a method of parameter learning by entropy minimization, and show the algorithm’s ability to perform feature selection. Promising experimental results are presented for synthetic data, digit classification, and text classification tasks. 1.
Reversal of drug sensitivity in multidrug-resistant tumor cells by an MDR1 (PGY1) ribozyme. (1994)

In order to reverse P-glycoprotein-mediated drug resistance in a specific manner, we designed two hammerhead ribozymes which can cleave the GUC sequence in codon 179 and 196 of MDR1 (PGY1) mRNA. The ribozymes were directly synthesized using a set of primers, one containing a bacteriophage T7 RNA polymerase promoter. A target MDR1 RNA was created by a reverse transcription polymerase chain reaction using a MOLT-3 human acute leukemia cell line resistant to trimetrexate (TMQ) (MOLT-3/TMQ800), which displayed MDR1 overexpression. In a cell-free system, both ribozymes cleaved a target piece of MDR1 RNA into 2 fragments at the specific sites at a physiological pH and temperature. The cleavage reaction was dependent on time, ribozyme:substrate ratio, and magnesium concentration. The 196 MDR1 ribozyme was more active than the 179 MDR1 ribozyme. The 196 MDR1 ribozyme was then cloned into a human expression vector, and MOLT-3/TMQ800 cells were transfected. The original MOLT-3/TMQ800 cells were nearly 700-fold resistant to vincristine, whereas the transfectant cells selected in G418 became only 20- to 30-fold resistant. The level of resistance and the amount of MDR1 RNA expressed appeared to correlate inversely with the amount of ribozyme expression. A disabled 196 MDR1 ribozyme was capable of neither specific cleavage in vitro nor decreasing MDR1 expression in transfectant cells. These results indicate that it was the ribozyme activity and not antisense activity which was responsible for decreased MDR1 RNA. This approach may be applicable to cancer patients as a specific means to reverse tumors with P-glycoprotein-mediated MDR phenotype back to a drug-sensitive one.
Circadian Uses of Melatonin in Humans (2006)

Melatonin in humans can be an independent or dependent variable. Measurement of endogenous melatonin levels under dim-light conditions, particularly the dim-light melatonin onset (DLMO), has received increasing attention among researchers, and for clinicians it may soon become a convenient test that can be done at home using saliva collections in the evening, without interfering with sleep. Melatonin, even at low physiological doses, can cause advances (shifts to an earlier time) or delays (shifts to a later time) depending on when it is administered on its phase-response curve (in most sighted people, these times are approximately in the p.m. and in the a.m., respectively). Although both bright light and melatonin can be used separately or together in the treatment of circadian phase disorders in sighted people-such as advanced and delayed sleep phase syndromes, jet lag, shift-work maladaptation, and winter depression (seasonal affective disorder, or SAD)-melatonin is the treatment of choice in totally blind people. These people provide a unique opportunity to study the human circadian system without the overwhelming effects of ocularly mediated light, thus permitting us to establish that all blind free-runners (BFRs) studied under high resolution appear to have phase-advancing and phase-delaying responses to as yet unidentified zeitgebers (time givers) that are usually too weak to result in entrainment.
Interferometric crosstalk-free optical add/drop multiplexer using Mach-Zehnder-based fiber gratings (1998)

Mach-Zehnder interferometers with fiber Bragg gratings (MZ-FG) are investigated as promising devices for wavelength-selectable optical add-and-drop multiplexers (OADM). A wavelength reused OADM performance is demonstrated for the first time to our knowledge in a six-channel, 10 Gb/s WDM experiment using a single-stage MZ-FG. We discuss both theoretically and experimentally the interferometric crosstalk induced by imperfect Bragg-reflectivity. Two methods are proposed to solve the interferometric crosstalk issues. The first one is wavelength offset scheme. It is experimentally confirmed that there is no interference when the wavelength of crosstalk is away from that of the signal at least two times of bit-rate. In order to separate each wavelength, the master-slave wavelength control method is proposed with Fabry-Perot interferometer made of a set of fiber gratings. The second one is a cascaded MZ-FG scheme eliminating the crosstalk itself. The calculation indicates that a Bragg-reflectivity of only 93% can suppress the crosstalk to be -35 dB. Cascaded MZ-FG's have been fabricated to show that the interferometric crosstalk can be successfully reduced to -50 dB for the add signal, and -71 dB for the drop signal, respectively. The eight-wavelength 10 Gb/s OADM experiment is carried out to demonstrate the low interferometric crosstalk performance.
Degeneracy and complexity in biological systems (2001)

Degeneracy, the ability of elements that are structurally different to perform the same function or yield the same output, is a well known characteristic of the genetic code and immune systems. Here, we point out that degeneracy is a ubiquitous biological property and argue that it is a feature of complexity at genetic, cellular, system, and population levels. Furthermore, it is both necessary for, and an inevitable outcome of, natural selection.
Embedded SRAM with O.5um CMOS Gate Array (1990)

otl terminals at every memory-cell boundar y. Prior to customizat iotl , first and second polysil icon are used to connect the internal memory cell nodes to the porl-customiza­ tion terminals. Multi-port SRAMs are configu red by first Al so that corresponding internal nodes of adjacent memory cells arc connected. At the same time, word lines are configured corresponding to the port customization using second Al and via hole. The use of second AI is a key to the density and speed. Figure 2 is a micrograph of memory cells which corresponds to two port configuration. A high-resistance polysilicon load cell is employed to provid e good write operation and high density. The cell size is 9x13.6um, one tenth the area of an equivalent mnItiport cell based on gate-array basic cells. The worst -case access speed of multi-port configuration based on this sch eme has no dependence on the number uf ports because tbe memory-cell current available to drive unit bit line load capacitance remains constant. In the multi-port configuration, the write operation from one port must flip all of the connecting cells through the NMOS transfer gate of the write port cell. Therefore a six-transistor full CMOS SRAM cell is not suitable for PC SRAM because PMOS transistors of cells which are not in the write port hind er
Current Spreading and Speech-Processing Strategies for Cochlear Prostheses (1987)

It is well known that current spreading in the cochlea causes a blurring at the excitable neural tissue of spatial details when the electrode array is stimulated. This paper describes techniques for compensating for current spreading by computing the pseudoinverse of the spreading function and applying a stimulation pattern to the electrode array, which produces the desired current pattern at the neural tissue. Specific examples are given assuming several current spreading functions, and the limits of applicability of the techniques in the domain of severe current spreading are explored.
Baiting Techniques for Control of Coptotermes Species Within Existing Buildings in Australia (1991)

Abstract: Baiting techniques have been developed over the years to control Coptotermes species, the most economically important termite species in Australia. Given the restrictions on organochlorines as termiticides in North America, this paper highlights research that has focussed on baiting programs against Coptotermes as alternatives to current control measures: drenching soil with pesticides or fumigation of entire structures. Details of the baiting procedures, toxins used, and their suitability for use in eradicating Coptotermes infestations in existing buildings are described. Suggestions are offered for the direction in which future baiting techniques may prove productive. In Australia subterranean termites cause most of the termite damage to timber in service (French 1986). Of these termites, the most economically important are the
Generic Security Service API : C-bindings (1993)

This RFC specifies an Internet standards track protocol for the Internet community, and requests discussion and suggestions for improvements.
A numerical investigation of nematic ordering based on a simple hard-rod model (1987)

On the basis of a simple functional scaling, we have constructed the direct generalization of the Carnahan–Starling equation for the free energy of a hard sphere fluid to a nematic liquid crystal. The orientational degrees of freedom are completely decoupled from translational ones under that scaling, which is equivalent to the well-known decoupling approximation for the pair correlation function of hard-core fluids. For long rods the generalized free energy reduces exactly to Onsager’s in the low density limit. Numerical calculations have been performed for a variety of the length-to-diameter ratios of hard spherocylinders, with the aid of an accurate iterative solution to the nonlinear integral equation for the orientational distribution function. The predictions made by our calculations are in fairly good agreement with the results of Monte Carlo simulations on a system of rather short rods. We present the calculations of the jump in the order parameter, critical packing fraciton, and the other thermodynamic properties at the isotropic–nematic transition.
Diazotransfer Reactions withp-Acetamidobenzenesulfonyl Azide (1987)

Abstract The utility of p-acetamidobenzenesulfonyl azide in diazotransfer reactions is described. This practical, cost effective reagent offers advantages over existing alternatives.
Temporal video segmentation using unsupervised clustering and semantic object tracking (1998)

The <i>Journal of Electronic Imaging</i> (JEI), copublished bimonthly with the Society for Imaging Science and Technology, publishes peer-reviewed papers that cover research and applications in all areas of electronic imaging science and technology.
Nanopore sculpting with noble gas ions (2006)

We demonstrate that 3 keV ion beams, formed from the common noble gasses, He, Ne, Ar, Kr, and Xe, can controllably "sculpt" nanometer scale pores in silicon nitride films. Single nanometer control of structural dimensions in nanopores can be achieved with all ion species despite a very wide range of sputtering yields and surface energy depositions. Heavy ions shrink pores more efficiently and make thinner pores than lighter ions. The dynamics of nanopore closing is reported for each ion species and the results are fitted to an adatom diffusion model with excellent success. We also present an experimental method for profiling the thickness of the local membrane around the nanopore based on low temperature sputtering and data is presented that provides quantitative measurements of the thickness and its dependence on ion beam species.
Blockade of interleukin-23 signaling results in targeted protection of the colon and allows for separation of graft-versus-host and graft-versus-leukemia responses (2010)

Allogeneic stem cell transplantation is the most potent form of effective adoptive immunotherapy. The graft-versus-leukemia (GVL) effect mediated by the allogeneic graft, however, is typically coexpressed with graft-versus-host disease (GVHD), which is the major complication of allogeneic stem cell transplantation. In this study, we used genetic and antibody-based strategies to examine the effect that blockade of interleukin 23 (IL-23) signaling had on GVH and GVL reactivity in murine transplantation recipients. These studies demonstrate that the selective protection of the colon that occurs as a consequence of inhibition of IL-23 signaling reduces GVHD without loss of the GVL effect. The separation of GVH and GVL reactivity was noted in both acute and chronic hematologic malignancy models, indicating that this approach was not restricted by the kinetic profile of the underlying leukemia. Furthermore, a potent GVL response could be mounted in the colon under conditions where tumor cells migrated to this site, indicating that this organ did not serve as a sanctuary site for subsequent systemic relapse in GVHD-protected animals. These studies demonstrate that blockade of IL-23 signaling is an effective strategy for separating GVH and GVL responses and identify IL-23 as a therapeutic target for the regulation of alloresponses in humans.
Inflammatory reaction after intrasynovial injection of microcrystalline adrenocorticosteroid esters (1964)

Abstract Injection of commercially available microcrystalline adrenocorticosteroid esters into normal canine joints was ac‐companied by a leukocyte‐rich exudative response, roughly proportional to the dose injected. No tenderness or evidence of pain was noted. Injection of these preparations into normal human joints often induced similar reactions which were sometimes painful. The response varied with the preparation employed and in the case of hydrocortisone acetate, with the manufacturer of the drug. The possible injurious effects of this relatively painless inflammatory response are discussed.
CVT transients revisited — Distance, directional overcurrent, and communications-assisted tripping concerns (2012)

Several classic papers explain the fundamentals of capacitive voltage transformer (CVT) design, operation, and transient response. Distance elements can overreach, particularly in high source-to-line impedance ratio (SIR) applications, which can result in undesired Zone 1 operations. Because this continues to be a problem in real applications, this paper revisits documented field cases using event data in hopes of shedding new light on this known problem. Solutions to distance element overreach are shared, from modified reach and time delays to modern solutions such as CVT transient detection logic. How does the protection engineer know what type of CVT is used? How can the protection engineer calculate the SIR from real-world event data? This paper gives practical guidance for the user to answer these fundamental questions. New data and research included in this paper update the topic. We investigate the CVT transient effect on directional element stability, directional overcurrent applications, and various communications-assisted protection schemes. We also share field cases of directional element and directional comparison blocking scheme misoperations and solutions and practical recommendations for mitigating the problems in all cases.
Interaction of the S phase regulator Cdc18 with cyclin-dependent kinase in fission yeast (1997)

The fission yeast gene cdc18(+) is required for entry into S phase and for coupling mitosis to the successful completion of S phase. Cdc18 is a highly unstable protein that is expressed only once per cell cycle at the G1/S boundary. Overexpression of Cdc18 causes a mitotic delay and reinitiation of DNA replication, suggesting that the inactivation of Cdc18 plays a role in preventing rereplication within a given cell cycle. In this paper, we present evidence that Cdc18 is associated with active cyclin-dependent kinase in vivo. We have expressed Cdc18 as a glutathione S-transferase fusion in fission yeast and demonstrated that the fusion protein is functional in vivo. We find that the Cdc18 fusion protein copurifies with a kinase activity capable of phosphorylating histone H1 and Cdc18. The activity was identified by a variety of methods as the cyclin-dependent kinase containing the product of the cdc2(+) gene. The amino terminus of Cdc18 is required for association with cyclin-dependent kinase, but the association does not require the consensus cyclin-dependent kinase phosphorylation sites in this region. Additionally, both G1/S and mitotic forms of cyclin-dependent kinase phosphorylate and interact with Cdc18. These interactions between Cdc18 and cyclin-dependent kinases suggest mechanisms by which cyclin-dependent kinases could activate the initiation of DNA replication and could prevent rereplication.
Safety, stability, and efficacy of noncapsulated mutants of Actinobacillus pleuropneumoniae for use in live vaccines (1993)

Clonal, noniridescent mutants of Actinobacillus pleuropneumoniae serotypes 1 and 5 were isolated following chemical mutagenesis with ethyl methanesulfonate. The absence of any detectable capsule was confirmed by inhibition radioimmunoassay. There were no differences between the parent and mutant strains in lipopolysaccharide or protein electrophoretic profiles or in hemolytic activity. There was no detectable reversion to the encapsulated phenotype in vitro after passage in mice or pigs or in microporous capsules that were implanted subcutaneously in pigs for 6 weeks. The mutants were able to survive for more than 1 week in pigs following subcutaneous inoculation, which resulted in a strong immune response to whole cells and Apx toxins I and II. Intratracheal challenge of pigs with the serotype 5 mutant at a dose 1 log greater than the 50% lethal dose for the parent resulted in no clinical disease or lesions except in one pig that had slight pneumonia and pleuritis. Twenty-four hours after challenge, A. pleuropneumoniae could not be recovered from the respiratory tracts of any of the challenged pigs except for the one infected pig; this isolate remained noncapsulated. Immunization of pigs with one or both serotypes of noncapsulated mutants protected all pigs against clinical disease following intratracheal challenge with the virulent homologous or heterologous serotype. Nonimmunized control pigs and pigs immunized with a commercial bacterin died or had to be euthanized within 24 h of challenge. Thus, live noncapsulated mutants of A. pleuropneumoniae may provide safe and cost-effective protection against swine pleuropneumonia. These observations support the possibility that noncapsulated mutants of other encapsulated, toxin-producing bacteria may also prove to be efficacious live-vaccine candidates.
Bacterial expression and secretion of various single-chain Fv genes encoding proteins specific for a Salmonella serotype B O-antigen. (1991)

Active single-chain Fv molecules encoded by synthetic genes have been expressed and secreted to the periplasm of Escherichia coli using the ompA secretory signal. Four different constructs were developed to investigate the effects of peptide linker design and VL-VH orientation on expression, secretion, and binding to a Salmonella O-polysaccharide antigen. Peptide linker sequences derived from the elbow regions of the Fab molecule were used alone or in combination with the flexible (GGGGS)2 sequence. VL and VH domain order in the single chain molecules had a profound effect on the level of secretion but hardly influenced total expression levels, which were approximately 50 mg/liter, chiefly in the form of inclusion bodies. With VL in the NH2-terminal position, the amount of secreted product obtained was 2.4 mg/liter, but when VH occupied this position the yield was less than 5% of this value. Enzyme immunoassays of the four products showed domain order and linker sequence affected antigen binding by less than an order of magnitude. Attempts to express active Fv from dicistronic DNA were unsuccessful, but active Fv was obtained from single-chain Fv by enzymic cleavage at a site in the elbow linker peptide. The thermodynamic binding parameters of intact and cleaved single-chain Fvs determined by titration microcalorimetry were similar to those of bacterially produced Fab and mouse IgG.