gebhart/patrepeval huggingface dataset:
Geomechanics-Reservoir Modeling by Displacement Discontinuity-Finite Element Method (2008)

There are two big challenges which restrict the extensive application of fully coupled geomechanics-reservoir modeling. The first challenge is computational effort. Consider a 3-D simulation combining pressure and heat diffusion, elastoplastic mechanical response, and saturation changes; each node has at least 5 degrees of freedom, each leading to a separate equation. Furthermore, regions of large p, T and σ′ gradients require small-scale discretization for accurate solutions, greatly increasing the number of equations. When the rock mass surrounding the reservoir region is included, it is represented by many elements or nodes. These factors mean that accurate analysis of realistic 3-D problems is challenging, and will so remain as we seek to solve larger and larger coupled problems involving nonlinear responses.&#13;\nTo overcome the first challenge, the displacement discontinuity method is introduced wherein a large-scale 3-D case is divided into a reservoir region where Δp, ΔT and non-linear effects are critical and analyzed using FEM, and an outside region in which the reservoir is encased where Δp and ΔT effects are inconsequential and the rock may be treated as elastic, analyzed with a 3D displacement discontinuity formulation. This scheme leads to a tremendous reduction in the degrees of freedom, yet allows for reasonably rigorous incorporation of the reactions of the surrounding rock. &#13;\nThe second challenge arises from some forms of numerical instability. There are actually two types of sharp gradients implied in the transient advection-diffusion problem: one is caused by the high Peclet numbers, the other by the sharp gradient which appears during the small time steps due to the transient solution. The way to eliminate the spurious oscillations is different when the sharp gradients are induced by the transient evolution than when they are produced by the advective terms, and existing literature focuses mainly on eliminating the spurious spatial temperature oscillations caused by advection-dominated flow.&#13;\nTo overcome the second challenge, numerical instability sources are addressed by introducing a new stabilized finite element method, the subgrid scale/gradient subgrid scale (SGS/GSGS) method.
Water-Soluble Ruthenium Alkylidenes:  Synthesis, Characterization, and Application to Olefin Metathesis in Protic Solvents (2000)

Ruthenium alkylidenes 6 and 7 bearing cationically functionalized phosphine ligands are soluble and stable in protic solvents and initiate olefin metathesis reactions in methanol, water, and aqueous emulsions. NMR spectroscopy data and X-ray diffraction analyses of alkylidene 6 suggested that these new alkylidenes were structurally similar to previously reported complexes of the type (PR3)2Cl2RuCHR, in which the alkylidene substituents lie in the Cl−Ru−Cl plane. The anionic chloride ligands of complexes 6 and 7 were found to undergo facile ligand exchange reactions with other anions in protic solution. Both alkylidenes initiate the ring-opening metathesis polymerization (ROMP) of strained, cyclic olefins in water. However, the propagating species in these reactions decompose prior to complete consumption of monomer. These complexes initiate the quantitative, living polymerization of functionalized monomers in water in the presence of a Brønsted acid. Both chain termination and chain transfer reactions were experimentally demonstrated to be absent on the time scale of these acid-activated polymerizations. Alkylidenes 6 and 7 react readily with acyclic olefins: alkylidene 6 reacted with trans-2-butene to yield a new ethylidene complex in either methanol or water, and the treatment of 6 with tri(ethylene glycol) methyl vinyl ether in water yielded water-soluble Fischer−carbene complex 16.
Light exposure stimulates formation of A2E oxiranes in a mouse model of Stargardt's macular degeneration (2004)

Recessive Stargardt's macular degeneration is a blinding disease of children caused by mutations in the ABCA4 (ABCR) gene. Mice with a knockout mutation in abcr accumulate toxic lipofuscin pigments in ocular tissues, similar to affected humans. The major fluorophore of lipofuscin is the bis-retinoid, N-retinylidene-N-retinylethanolamine (A2E). In the current study, we sought to define the effect of increasing light on A2E accumulation. We crossed the abcr(-/-) mutation onto an albino background. The retinoid profiles in albino mice indicated higher retinal illuminance than in pigmented mice exposed to similar ambient light. Unexpectedly, A2E levels were not higher in the albino mice. Also, A2E levels in abcr(-/-) mice reared under cyclic light at 30, 120, or 1,700 lux were similar. Thus, increased retinal illuminance was not correlated with higher A2E. A2E has been shown to undergo light-dependent oxidation to yield a series of A2E epoxides or oxiranes. These oxiranes react with DNA in vitro, suggesting a potential mechanism for A2E cytotoxicity. We analyzed ocular tissues from abcr(-/-) mice for A2E oxiranes by mass spectrometry. Unlike A2E, the oxiranes were more abundant in albino vs. pigmented abcr(-/-) mice, and in abcr(-/-) mice exposed to increasing ambient light. These observations suggest that both the biosynthesis of A2E and its conversion to oxiranes are accelerated by light. Finally, we showed that the formation of A2E oxiranes is strongly suppressed by treating the abcr(-/-) mice with Accutane (isotretinoin), an inhibitor of rhodopsin regeneration.
The hematopoietic stem cell niche: Low in oxygen but a nice place to be (2009)

The enormous regenerative capacity of the blood system to sustain functionally mature cells are generated from highly proliferative, short-lived progenitors, which in turn arise from a rare population of pluripotent and self-renewing hematopoietic stem cells (HSC). In the bone marrow, these stem cells are kept in a low proliferative, relatively quiescent state in close proximity to stromal cells and osteoblasts, forming specialized niches. The interaction in particular to bone is crucial to prevent exhaustion of HSCs from uncontrolled cell-cycle entry and to excessive proliferation. In addition, the niche and its components protect stem cells from stress, such as accumulation of reactive oxygen species and DNA damage. One of the key issues is to identify conditions to increase the number of HSCs, either in vivo or during ex vivo growth cultures. This task has been very difficult to resolve and most attempts have been unsuccessful. However, the mechanistic insights to HSC self-renewal and preservation are gradually increasing and there is now hope that future research will enable scientists and clinicians to modulate the process. In this review, we will focus on the molecular mechanisms of self-renewal and HSC maintenance in the light of novel findings that HSCs reside at the lowest end of an oxygen gradient. Hypoxia appears to regulate hematopoiesis in the bone marrow by maintaining important HSC functions, such as cell cycle control, survival, metabolism, and protection against oxidative stress. To improve the therapeutic expansion of HSCs we need to learn more about the molecular mechanisms of hypoxia-mediated regulation.
Zinc deficiency worsens ethanol-induced gastric ulcers in rats. (1988)

The effects of zinc deficiency on ethanol-induced ulcers were studied. Rats fed with zinc-deficient diets for 5 weeks showed markedly lowered serum zinc levels and body weights. Ethanol 30% given orally produced gastric mucosal lesions and reduced the glutathione content in the gastric glandular mucosa in their pair-fed non-zinc-deficient controls. Zinc deficiency potentiated the glutathione-depleting and ulcer-producing effects of ethanol. N-acetylcysteine, a sulfhydryl-containing agent, protected non-zinc-deficient rats from lesions produced by 50% ethanol, whereas N-ethylmaleimide, a sulfhydryl-blocking agent, worsened ulceration. It appears that zinc deficiency intensifies ethanol-induced ulceration by permitting greater depletion of the glutathione content in the stomach.
Isolation and characterization of SRF accessory proteins (1993)

Many genes which are regulated by growth factors contain a common regulatory element, the serum response element (SRE). Activation of transcription by the SRE involves a ternary complex formed between a ubiquitous factor, serum response factor (SRF), and a second protein, p62/TCF. We used a yeast genetic screen to isolate cDNAs encoding a protein, SAP-1, with the DNA binding properties of p62/TCF. The SAP-1 sequence contains three regions of homology to the previously uncharacterized Elk-1 protein, which also acts as an SRF accessory protein. Only two of these regions are required for cooperative interactions with SRF in the ternary complex. The third contains several conserved sites for the MAP kinases, whose activity is regulated in response to growth factor stimulation. We discuss the potential role of these proteins in regulation of the c-fos SRE.
RNA Extraction From Mammalian Tissues (2007)

Purification of intact RNA is the primary step of many molecular biology techniques, including Northern blotting, RNase protection, quantitative polymerase chain reaction, and microarray assays. RNA extraction is typically conducted using either a phenol-chloroform or a solid phase method. This article concentrates primarily on the former approach, which is highly versatile, and is easily adapted to different tissues ranging from whole organs down to submillimeter biopsy punches. The major problem with RNA extraction is the ubiquitous nature of RNases, enzymes that rapidly degrade RNA. RNases may be difficult to eliminate, although with care and appropriate countermeasures, reproducible extraction of high-quality RNA from important biological samples should be attainable. This article focuses on the isolation of RNA from the tissue collection step, homogenization all the way through to the quantification of the purified nucleic acid, providing guidelines for the prevention of the problems associated with RNAse contamination.
Marked Prolongation of Cardiac Allograft Survival by Dendritic Cells Genetically Engineered with NF-κB Oligodeoxyribonucleotide Decoys and Adenoviral Vectors Encoding CTLA4-Ig (2002)

Bone marrow-derived dendritic cells (DCs) can be genetically engineered using adenoviral (Ad) vectors to express immunosuppressive molecules that promote T cell unresponsiveness. The success of these DCs for therapy of allograft rejection has been limited in part by the potential of the adenovirus to promote DC maturation and the inherent ability of the DC to undergo maturation following in vivo administration. DC maturation occurs via NF-kappaB-dependent mechanisms, which can be blocked by double-stranded "decoy" oligodeoxyribonucleotides (ODNs) containing binding sites for NF-kappaB. Herein, we describe the combined use of NF-kappaB ODNs and rAd vectors encoding CTLA4-Ig (Ad CTLA4-Ig) to generate stably immature murine myeloid DCs that secrete the potent costimulation blocking agent. These Ad CTLA4-Ig-transduced ODN DCs exhibit markedly impaired allostimulatory ability and promote apoptosis of activated T cells. Furthermore, administration of Ad CTLA4-Ig ODN-treated donor DCs (C57BL10; B10(H-2b)) before transplant significantly prolongs MHC-mismatched (C3HHeJ; C3H(H-2k)) vascularized heart allograft survival, with long-term (>100 days) donor-specific graft survival in 40% of recipients. The mechanism(s) responsible for DC tolerogenicity, which may involve activation-induced apoptosis of alloreactive T cells, do not lead to skewing of intragraft Th cytokine responses. Use of NF-kappaB antisense decoys in conjunction with rAd encoding a potent costimulation blocking agent offers promise for therapy of allograft rejection or autoimmune disease with minimization of systemic immunosuppression.
The fragile X mental retardation protein is a ribonucleoprotein containing both nuclear localization and nuclear export signals (1996)

Fragile X syndrome is a frequent cause of mental retardation resulting from the absence of FMRP, the protein encoded by the FMR1 gene. FMRP is an RNA-binding protein of unknown function which is associated with ribosomes. To gain insight into FMRP function, we performed immunolocalization analysis of FMRP truncation and fusion constructs which revealed a nuclear localization signal (NLS) in the amino terminus of FMRP as well as a nuclear export signal (NES) encoded by exon 14. A 17 amino acid peptide containing the FMRP NES, which closely resembles the NES motifs recently described for HIV-1 Rev and PKI, is sufficient to direct nuclear export of a microinjected protein conjugate. Sucrose gradient analysis shows that FMRP ribosome association is RNA-dependent and FMRP is found in ribonucleoprotein (RNP) particles following EDTA treatment. These data are consistent with nascent FMRP entering the nucleus to assemble into mRNP particles prior to export back into the cytoplasm and suggests that fragile X syndrome may result from altered translation of transcripts which normally bind to FMRP.
Cell-cell contact of human T cells with fibroblasts changes lymphocytic mRNA expression: increased mRNA expression of interleukin-17 and interleukin-17 receptor. (2000)

Using random arbitrarily primed-reverse transcribed-PCR and sequence analysis, we investigated changes in lymphocytic molecules after cell-cell contact with fibroblasts. An mRNA species which was upregulated in Jurkat T cells by cell-cell contact with MRHF cells (a human foreskin fibroblast line) was identified as coding for the human interleukin-17 receptor. This finding was confirmed by quantitative RT-PCR for the HUT78 and Jurkat T cell lines, for peripheral blood lymphocytes, and for tonsillar T cells. Furthermore, the interleukin-17 mRNA, coding for a proinflammatory cytokine, was also upregulated in peripheral blood lymphocytes and tonsillar T cells after cell-cell contact with fibroblasts. Supernatants obtained from cell-cell contact-stimulated peripheral blood lymphocytes enhance the production of interleukin-6 and interleukin-8 by fibroblast-like synoviocytes and this effect could be blocked by interleukin-17 antibodies. Changes in the mRNA levels of Jurkat T cells induced by cell-cell contact with adherent cells were also found for M-type pyruvate kinase, for tropomyosin TM30 and for the p54nrb gene product.
Hyperspectral Imaging: A New Approach to the Diagnosis of Hemorrhagic Shock (2006)

HSI is a promising noninvasive and noncontact tool for quantifying changes in skin oxygenation during HEM and resuscitation.
Osteoinductivity of Demineralized Bone Matrix Is Independent of Donor Bisphosphonate Use (2011)

Demineralized bone matrix samples from donors treated with bisphosphonates and donors not treated with bisphosphonates have the same ability to induce bone formation. However, it is not known if the quality of the new bone is affected, with subsequent consequences affecting bone remodeling.
Blockade of receptors for growth factors: an anticancer therapy--the fourth annual Joseph H Burchenal American Association of Cancer Research Clinical Research Award Lecture. (2000)

Dr. Daniel von Hoff, thank you for that marvelous introduction. In the first row at this American Association for Cancer Research meeting today are Dr. and Mrs. Joseph Burchenal. It is a special privilege for me to be honored with this award named after him because he started the medical oncology
Inactivated Venezuelan Equine Encephalomyelitis Virus Vaccine Complexed with Specific Antibody: Enhanced Primary Immune Response and Altered Pattern of Antibody Class Elicited (1977)

Complexes of formalinized Venezuelan equine encephalomyelitis (VEE) virus vaccine and specific IgG formed at antigen-antibody equivalence enhanced the immune responses of rhesus monkeys (Macaca mulatta). The predomonant class of antibody elicited by complexes was IgG. In contrast, lower titers of antibody and a more biphasic (IgG-IgM) response were observed after exposure of monkeys to the vaccine alone. In comparison to the response of monkeys primed with antigen, a more rapid secondary response was obtained in monkeys primed with the complexes of antigen and antibody formed at equivalence. A sustained level of protection of 88% was afforded mice 24 hr after immunization with antigen-antibody complexes; development of protection after administration of antigen required eight days to reach this level. Passive protection (80%-100%) was conferred by IgG controls for seven to eight days after immunization. This level of protection was not significantly affected by X-irradiation 24 hr prior to administration of IgG; however, protection in mice similarly irradiated prior to immunization with antigen-antibody complexes was significantly decreased. Early protection afforded by the complexes was not nonspecific (interferon) but was mediated by specific immunologic mechanisms and may be caused by an early formation of IgG.
Adaptive data refinement in the spectral stochastic finite element method (2002)

Abstract One version of the stochastic finite element method involves representing the solution with respect to a basis in the space of random variables and evaluating the co‐ordinates of the solution with respect to this basis by relying on Hilbert space projections. The approach results in an explicit dependence of the solution on certain statistics of the data. The error in evaluating these statistics, which is directly related to the amount of available data, can be propagated into errors in computing probabilistic measures of the solution. This provides the possibility of controlling the approximation error, due to limitations in the data, in probabilistic statements regarding the performance of the system under consideration. In addition to this error associated with data resolution, is added the more traditional error, associated with mesh resolution. This latter also contributes to polluting the estimated probabilities associated with the problem. The present paper will develop the above concepts and indicate how they can be coupled in order to yield a more meaningful and useful measure of approximation error in a given problem. Copyright © 2002 John Wiley &amp; Sons, Ltd.
Musical emotions: Predicting second-by-second subjective feelings of emotion from low-level psychoacoustic features and physiological measurements. (2011)

We sustain that the structure of affect elicited by music is largely dependent on dynamic temporal patterns in low-level music structural parameters. In support of this claim, we have previously provided evidence that spatiotemporal dynamics in psychoacoustic features resonate with two psychological dimensions of affect underlying judgments of subjective feelings: arousal and valence. In this article we extend our previous investigations in two aspects. First, we focus on the emotions experienced rather than perceived while listening to music. Second, we evaluate the extent to which peripheral feedback in music can account for the predicted emotional responses, that is, the role of physiological arousal in determining the intensity and valence of musical emotions. Akin to our previous findings, we will show that a significant part of the listeners' reported emotions can be predicted from a set of six psychoacoustic features--loudness, pitch level, pitch contour, tempo, texture, and sharpness. Furthermore, the accuracy of those predictions is improved with the inclusion of physiological cues--skin conductance and heart rate. The interdisciplinary work presented here provides a new methodology to the field of music and emotion research based on the combination of computational and experimental work, which aid the analysis of the emotional responses to music, while offering a platform for the abstract representation of those complex relationships. Future developments may aid specific areas, such as, psychology and music therapy, by providing coherent descriptions of the emotional effects of specific music stimuli.
Amides as Substitute for the Phosphodiester Linkage in Antisense Oligonucleotides (1993)

The synthesis of a thymidine dimer in which the natural phosphodiester linkage has been replaced by an amide (3′-CH2-CH2-NH-CO-4′) is described. This new dimer was incorporated into oligonucleotides. Measurement of melting temperatures (Tm) of DNA/RNA duplexes and the nuclease resistance are presented. Preliminary results of molecular mechanics are included.
Development of a capillary high-performance liquid chromatography tandem mass spectrometry system using SWIFT technology in an ion trap/reflectron time-of-flight mass spectrometer (1997)

In this work a capillary high-performance liquid chromatography/tandem mass spectrometry system has been developed in a quadrupole ion trap/reflectron time-of-flight mass spectrometer. The broadband excitation for isolating a precursor ion is achieved by generating the stored waveform inverse Fourier transform waveform in real time. Following the isolation and cooling periods, an auxiliary AC voltage (tickle) is applied to the entrance end cap of the ion trap to generate collision induced dissociation. The amplitude of the tickle voltage is optimized on-line using a feedback method which involves having two computers communicating with each other. This system has been tested with a 4-peptide mixture and tandem mass spectra were obtained for each peptide.
Marked replicative advantage of human mtDNA carrying a point mutation that causes the MELAS encephalomyopathy. (1992)

The segregation of mutant and wild-type mtDNA was investigated in transformants constructed by transferring human mitochondria from individuals belonging to four pedigrees with the MELAS encephalomyopathy-associated mtDNA mutation (MELAS is mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes) into human mtDNA-less (rho 0) cells. Five of 13 clonal cell lines containing mixtures of wild-type and mutant mtDNAs were found to undergo a rapid shift of their genotype toward the pure mutant type. The other 8 cell lines, which included 6 exhibiting nearly homoplasmic mutant mtDNA, on the contrary, maintained a stable genotype. Subcloning experiments and growth rate measurements clearly indicated that an intracellular replicative advantage of mutant mtDNA was mainly responsible for the dramatic shift toward the mutant genotype observed in the unstable cell lines.
A three‐symbol code for organized proteomes based on cyclical imaging of protein locations (2007)

The technology has the potential to colocalize hundreds of proteins and other molecular components in one sample and may offer many applications in biology and medicine.
NAD+-malic enzyme. Regulatory properties of the enzyme from Ascaris suum. (1976)

The regulatory properties of the NAD-dependent malic enzyme from the mitochondria of Ascaris suum have been studied. The malate saturation curve exhibits sigmoidicity and the degree of this sigmoidicity increases as the pH is increased. Fumarate was the only compound tested that stimulated the enzyme activity, whereas oxalacetate was the most powerful inhibitor. Activation by low levels of fumarate was found to be competitive with malate. It is proposed that this stimulation has physiological significance in controlling the dismutation reaction in the parasite. The branched-chain volatile fatty acid excretion products, tiglate, 2-methylbutanoate, and 2-methylpentanoate, inhibited the enzyme activity and this inhibition was competitive with malate. The Ki values for these compounds are in the physiological range of their concentrations; therefore, it is suggested that they may aid in controlling the malic enzyme activity in vivo. Oxalacetate inhibition of malic enzyme activity was competitive with malate, and the Ki values decreased with an increase in pH. Two alternatives are proposed which could account for the lack of oxalacetate decarboxylation by the ascarid malic enzyme.