gebhart/patrepeval huggingface dataset:
Complete measurement of spatiotemporally complex multi-spatial-mode ultrashort pulses from multimode optical fibers using delay-scanned wavelength-multiplexed holography (2017)

We introduce a simple delay-scanned complete spatiotemporal intensity-and-phase measurement technique based on wavelength-multiplexed holography to characterize long, complex pulses in space and time. We demonstrate it using pulses emerging from multi-mode fiber. This technique extends the temporal range and spectral resolution of the single-frame STRIPED FISH technique without using an otherwise-required expensive ultranarrow-bandpass filter. With this technique, we measured the complete intensity and phase of up to ten fiber modes from a multi-mode fiber (normalized frequency V ≈10) over a ~3ps time range. Spatiotemporal complexities such as intermodal delay, modal dispersion, and material dispersion were also intuitively displayed by the retrieved results. Agreement between the reconstructed color movies and the monitored time-averaged spatial profiles confirms the validity to this delay-scanned STRIPED FISH method.
Optical Amplification of Ligand-Receptor Binding Using Liquid Crystals (1998)

Liquid crystals (LCs) were used to amplify and transduce receptor-mediated binding of proteins at surfaces into optical outputs. Spontaneously organized surfaces were designed so that protein molecules, upon binding to ligands hosted on these surfaces, triggered changes in the orientations of 1- to 20-micrometer-thick films of supported LCs, thus corresponding to a reorientation of approximately 10(5) to 10(6) mesogens per protein. Binding-induced changes in the intensity of light transmitted through the LC were easily seen with the naked eye and could be further amplified by using surfaces designed so that protein-ligand recognition causes twisted nematic LCs to untwist. This approach to the detection of ligand-receptor binding does not require labeling of the analyte, does not require the use of electroanalytical apparatus, provides a spatial resolution of micrometers, and is sufficiently simple that it may find use in biochemical assays and imaging of spatially resolved chemical libraries.
Programmed cell death as a new target for prostatic cancer therapy. (1991)

To increase survival of men with metastatic prostatic cancer, a modality that can effectively eliminate androgen independent cancer cells is desperately needed. By combining such an effective modality with androgen ablation, all of the heterogeneous populations of tumour cells within a prostatic cancer patient can be affected, thus optimizing the chances of cure. Unfortunately, such effective therapy for the androgen independent prostatic cancer cell is not yet available. This therapy will probably require two types of agents, one having antiproliferative activity affecting the small number of dividing androgen independent cells, and the other able to increase the low rate of cell death among the majority of non-proliferating (ie interphase) androgen independent prostatic cancer cells present. Androgen dependent prostatic epithelial cells can be made to undergo programmed death by means of androgen ablation, even if the cells are not in the proliferative cell cycle. Androgen independent prostatic cancer cells retain the major portion of this programmed cell death pathway, only there is a defect in the pathway such that it is no longer activated by androgen ablation. If the intracellular free Ca2+ is sustained at an elevated level for a sufficient time, androgen independent cells can be induced to undergo programmed death. The long term goal is therefore to develop some type of non-androgen ablative method that can be used in vivo to induce a sustained elevation in Ca2+ in androgen independent prostatic cancer cells. To accomplish this task, a more complete understanding of the biochemical pathways involved in programmed cell death is urgently needed. At present, studies are focusing on the mechanism involved in the Ca2+ elevation in the normal and malignant androgen dependent cell induced following androgen ablation and the role of the TRPM-2 protein in this process.
Expression of CA III in Rodent Models of Obesity (1991)

To achieve a better understanding of the biochemical basis of obesity, we have undertaken comparative analyses of adipose tissue of lean and obese mice. By two-dimensional gel analysis, carbonic anhydrase-III (CA III) has been identified as a major constituent of murine adipose tissue. Quantitative comparisons of CA III protein and mRNA levels indicate that this enzyme is expressed at lower levels in adipose tissue from animals that were either genetically obese or had experimentally induced obesity compared to levels in the corresponding lean controls. This decrease in CA III expression was unique to adipose tissue, since other CA III-containing organs and tissues did not show a change when lean and obese animals were compared. Additionally, levels of CA III in adipose tissue from obese animals responded to acute changes in energy balance of the animal. These results are discussed in light of possible metabolic roles for CA III.
GENETICS OF EXTRACELLULAR PROTEIN SECRETION BY GRAM-NEGATIVE BACTERIA (1990)

Orthologs and paralogs are two fundamentally different types of homologous genes that evolved, respectively, by vertical descent from a single ancestral gene and by duplication. Orthology and paralogy are key concepts of evolutionary genomics. A ...Read More
Broad phase II study of vindesine. (1981)

A broad phase II study of vindesine was conducted in 79 adults with advanced malignancies. Most patients had solid tumors, particularly adenocarcinomas (59%), and 67 patients had received prior chemotherapy which included vincristine in 24 patients and vinblastine in one. Depending on tolerance to previous therapy, patients received vindesine at doses of 3-4 mg/m2 administered iv at 2-week intervals. Objective tumor regressions were seen in eight of 36 patients (one complete response, one partial response [PR], and six minor responses) with colorectal cancer, one of four patients (PR) with squamous cell cancer of the esophagus, one of four patients (PR) with malignant melanoma, and one of two patients (PR) with lymphoma. Five of 11 responding patients had received vincristine previously. Toxic effects were manageable. The results of this study justify in-depth, disease-oriented phase II evaluations of vindesine, regardless of prior therapy with other vinca alkaloids.
Complement-Dependent P-Selectin Expression and Injury following Ischemic Stroke (2006)

Abstract The mechanisms that contribute to inflammatory damage following ischemic stroke are poorly characterized, but studies indicate a role for both complement and P-selectin. In this study, we show that compared with wild-type mice, C3-deficient mice showed significant improvement in survival, neurological deficit, and infarct size at 24 h after middle cerebral artery occlusion and reperfusion. Furthermore, P-selectin protein expression was undetectable in the cerebral microvasculature of C3-deficient mice following reperfusion, and there was reduced neutrophil influx, reduced microthrombus formation, and increased blood flow postreperfusion in C3-deficient mice. We further investigated the use of a novel complement inhibitory protein in a therapeutic paradigm. Complement receptor 2 (CR2)-Crry inhibits complement activation at the C3 stage and targets to sites of complement activation. Treatment of normal mice with CR2-Crry at 30 min postreperfusion resulted in a similar level of protection to that seen in C3-deficient mice in all of the above-measured parameters. The data demonstrate an important role for complement in cerebrovascular thrombosis, inflammation, and injury following ischemic stroke. P-selectin expression in the cerebrovasculature, which is also implicated in cerebral ischemia and reperfusion injury, was shown to be distal to and dependent on complement activation. Data also show that a CR2-targeted approach of complement inhibition provides appropriate bioavailability in cerebral injury to enable complement inhibition at a dose that does not significantly affect systemic levels of serum complement activity, a potential benefit for stroke patients where immunosuppression would be undesirable due to significantly increased susceptibility to lung infection.
Effect of Concomitant Icosapent Ethyl (Eicosapentaenoic Acid Ethyl Ester) on the Pharmacokinetics of Atorvastatin (2014)

At steady-state concentrations, icosapent ethyl did not have an effect on the pharmacokinetics of atorvastatin. Co-administration of icosapent ethyl and atorvastatin was safe and well tolerated in healthy adult subjects.
Complete structure of the mouse mast cell receptor for IgE (Fc ϵ RI) and surface expression of chimeric receptors (rat-mouse-human) on transfected cells (1989)

The high affinity receptor for IgE (Fc epsilon RI) found on mast cells and basophils is a tetrameric complex of a single alpha subunit, a single beta subunit, and two identical gamma subunits. The genes for the three subunits of mouse Fc epsilon RI have now been cloned from the mast cell line, PT18. When compared at the DNA level, the rat and mouse subunits are similarly conserved. However, at the protein level the homology between mouse and rat alpha is surprisingly low (71% identities) especially in the cytoplasmic regions (57% identities) which are of different length (25 and 20 residues, respectively). By contrast the beta and gamma are homogeneously conserved between mouse and rat (83 and 93% identities, respectively). The consensus amino acid sequence of the alpha subunit derived from three species (rat, mouse, and human) shows that the cytoplasmic tail diverges to the same extent as the leader peptide. Conversely, the transmembrane domain of the alpha is highly conserved and contains 10 consecutive residues that are identical. Comparisons between mouse Fc epsilon RI and other mouse proteins reveal regions of high homology between the alpha subunit and Fc gamma RIIa and between the gamma subunit and the zeta chain of the T cell receptor. Cells transfected with the alpha gene express the alpha subunit on their surface very inefficiently. Efficient expression is only achieved after co-transfection of the three rodent genes or of the human alpha gene together with the rodent gamma without apparent need for beta. The subunits are completely interchangeable upon transfection so that various chimeric mouse-rat-human receptors can be expressed.
Comparison of the Acetyl Bromide Spectrophotometric Method with Other Analytical Lignin Methods for Determining Lignin Concentration in Forage Samples (2004)

Present analytical methods to quantify lignin in herbaceous plants are not totally satisfactory. A spectrophotometric method, acetyl bromide soluble lignin (ABSL), has been employed to determine lignin concentration in a range of plant materials. In this work, lignin extracted with acidic dioxane was used to develop standard curves and to calculate the derived linear regression equation (slope equals absorptivity value or extinction coefficient) for determining the lignin concentration of respective cell wall samples. This procedure yielded lignin values that were different from those obtained with Klason lignin, acid detergent acid insoluble lignin, or permanganate lignin procedures. Correlations with in vitro dry matter or cell wall digestibility of samples were highest with data from the spectrophotometric technique. The ABSL method employing as standard lignin extracted with acidic dioxane has the potential to be employed as an analytical method to determine lignin concentration in a range of forage materials. It may be useful in developing a quick and easy method to predict in vitro digestibility on the basis of the total lignin content of a sample.
Single-shot real-time characterization of chirped-pulse amplification systems by spectral phase interferometry for direct electric-field reconstruction (1999)

We characterize chirped-pulse amplification systems by using spectral phase interferometry for direct electric-field reconstruction. For the first time to the authors' knowledge, single-shot real-time operation has been obtained for this technique, leading to a fast and accurate optimization of these systems.
Superoxide dismutase: an evolutionary puzzle. (1985)

We have obtained the complete amino acid sequence of copper/zinc-containing superoxide dismutase (SOD, superoxide:superoxide oxidoreductase, EC 1.15.1.1) from Drosophila melanogaster. The sequence of this enzyme is also known for man, horse, cow, and the yeast Saccharomyces cerevisiae. The rate of evolution of this enzyme is far from constant. The number of amino acid substitutions per 100 residues per 100 million years is 30.9 when the three mammals are compared to each other, 10.6 when Drosophila is compared to the three mammals, and 5.8 when the yeast is compared to the four animals. The first value represents one of the fastest evolutionary rates for any protein, the second is similar to the globin rate, and the third is similar to some cytochromes and other slowly evolving proteins. Hence, SOD is not an acceptable evolutionary clock. Another peculiarity of this enzyme is that a two-amino-acid deletion must have occurred independently in the lineages going to the cow and to Drosophila. We conclude that using the primary structure of a single gene or protein to time evolutionary events or to reconstruct phylogenetic relationships is potentially fraught with error.
A New Technology for Stabilization of Biomolecules in Tissues for Combined Histological and Molecular Analyses (2012)

For accurate diagnosis, prediction of outcome, and selection of appropriate therapies, the molecular characterization of human diseases requires analysis of a broad spectrum of altered biomolecules, in addition to morphological features, in affected tissues such as tumors. In a high-throughput screening approach, we have developed the PAXgene Tissue System as a novel tissue stabilization technology. Comprehensive characterization of this technology in stabilized and paraffin-embedded human tissues and comparison with snap-frozen tissues revealed excellent preservation of morphology and antigenicity, as well as outstanding integrity of nucleic acids (genomic DNA, miRNA, and mRNA) and phosphoproteins. Importantly, PAXgene-fixed, paraffin-embedded tissues provided RNA quantity and quality not only significantly better than that obtained with neutral buffered formalin, but also similar to that from snap-frozen tissue, which currently represents the gold standard for molecular analyses. The PAXgene tissue stabilization system thus opens new opportunities in a variety of molecular diagnostic and research applications in which the collection of snap-frozen tissue is not feasible for medical, logistic, or ethical reasons. Furthermore, this technology allows performing histopathological analyses together with molecular studies in a single sample, which markedly facilitates direct correlation of morphological disease phenotypes with alterations of nucleic acids and other biomolecules.
Suppression of Invasion by Inducible Expression of Tissue Inhibitor of Metalloproteinase-1 (TIMP-1) in B 16-F10 Melanoma Cells (1992)

Our data demonstrate that a specific upregulation of murine TIMP-1 expression in B16-F10 melanoma cells directly suppresses their invasive ability.
Activation of the alternative complement pathway by EBV and the viral envelope glycoprotein, gp350. (1988)

The EBV-producing B lymphoblastoid cell line B95-8 was found to efficiently activate the alternative C pathway whether assessed with Mg-EGTA-treated human serum or with mixtures of the purified proteins of the pathway (PAP). The ability of the cells to activate was markedly increased after stimulation of EBV replication by treatment of the cells with a phorbol ester, and decreased by treatment of the cells with a viral polymerase inhibitor. Alternative pathway activation was dependent on the presence of either properdin or EBV-immune IgG; the addition of either alone to the PAP led to the deposition of 200,000 C3 molecules/cell. The addition of both properdin and immune IgG to the PAP markedly increased C3 binding to a level of 800,000 molecules/cell. Several lines of evidence indicate that the major external glycoprotein of EBV, gp350, mediates alternative pathway activation by B95-8 cells. First, the ability to activate C positively correlated with gp350 expression on the surface of the EBV-producing cells and gp350- cells failed to activate; second, the anti-EBV antibody in immune human sera which enhanced activation specifically immunoprecipitated gp350 from membranes of B95-8 cells; third, a significant proportion of the C3 which became bound to the cells during activation was attached either to gp350 or to the anti-gp350 antibody found in immune human sera; and fourth, purified gp350, as well as EBV, efficiently activated the alternative pathway. These results indicate that gp350, an EBV envelope glycoprotein, is an efficient alternative pathway activator and its expression on cell membranes is associated with the ability to activate C.
Intramolecular integration within Moloney murine leukemia virus DNA (1981)

By screening a library of unintegrated, circular Moloney murine leukemia virus (M-MuLV) DNA cloned in lambda phage, we found that approximately 20% of the M-MuLV DNA inserts contained internal sequence deletions or inversions. Restriction enzyme mapping demonstrated tht the deleted segments frequently abutted a long terminal repeat (LTR) sequence, whereas the inverted segments were usually flanked by LTR sequences, suggesting that many of the variants arose as a consequence of M-MuLV DNA molecules integrating within their own DNA. Nucleotide sequencing also suggested that most of the variant inserts were generated by autointegration. One of the recombinant M-MuLV DNA inserts contained a large inverted repeat of a unique M-MuLV sequence abutting an LTR. This molecule was shown by nucleotide sequencing to have arisen by an M-MuLV DNA Molecule integrating within a second M-MuLV DNA molecule before cloning. The autointegrated M-MuLV DNA had generally lost two base pairs from the LTR sequence at each junction with target site DNA, whereas a four-base-pair direct repeat of target site DNA flanked the integrated viral DNA. Nucleotide sequencing of preintegration target site DNA showed that this four-base-pair direct repeat was present only once before integration and was thus reiterated by the integration event. The results obtained from the autointegrated clones were supported by nucleotide sequencing of the host-virus junction of two cloned M-MuLV integrated proviruses obtained from infected rat cells. Detailed analysis of the different unique target site sequences revealed no obvious common features.
Changes in mood and hormone levels after rapid-rate transcranial magnetic stimulation (rTMS) of the prefrontal cortex (1996)

Rapid-rate transcranial magnetic stimulation (rTMS) was administered to 10 healthy volunteers on different days over the right or left prefrontal cortex, midfrontal cortex, occipital cortex, or cerebellum. Mood (self-rated), reaction time, and hormone levels were serially measured. Consistent with a previous study, comparison of hemispheres revealed significant associations with decreased happiness after left prefrontal rTMS and decreased sadness after right prefrontal rTMS. Stimulation of all three prefrontal regions, but not the occipital or cerebellar regions, was associated with increases in serum thyroid-stimulating hormone. There was no effect on serum prolactin. rTMS applied to prefrontal cortex is safe and well tolerated and produces regionally and laterally specific changes in mood and neuroendocrine measures in healthy adults. rTMS is a promising tool for investigating prefrontal cortex functions.
Tertiary Amine‐Catalyzed Difluoromethylthiolation of Morita–Baylis–Hillman Carbonates of Isatins with Zard's Trifluoromethylthiolation Reagent (2016)

Abstract In this paper, we report that a novel tertiary amine‐catalyzed [3+2] annulation between Morita–Baylis–Hillman (MBH) carbonates derived from isatins with thiocarbonyl fluoride (F 2 C=S) in situ generated from Zard's reagent proceeds smoothly under mild conditions, affording difluoromethylthiolated spirocyclic oxindoles in good to excellent yields. Moreover, the asymmetric variant could be realized with a modified Cinchona alkaloid, giving the desired cyclic adducts in good to excellent yields with good enantioselectivities. magnified image
Synthesis of peptidyl fluoromethyl ketones and peptidyl .alpha.-keto esters as inhibitors of porcine pancreatic elastase, human neutrophil elastase, and rat and human neutrophil cathepsin G (1990)

Comparison of MeO-Suc-Val-Pro-Phe-CO2Me (29) and MeO-Suc-Ala-Ala-Pro-Phe- CO2Me (25) with their corresponding trifluoromethyl ketones 9a and 9b, respectively, in rat and human neutrophil cathepsin G assays showed the alpha-keto esters to be more potent inhibitors. Likewise, Ac-Pro-Ala-Pro-Ala-CO2Me (21) was more potent than its corresponding trifluoromethyl ketone (9c) in both porcine pancreatic elastase and human neutrophil elastase assays. Within a set of Ala-Ala-Pro-Val-CF3 elastase inhibitors, the carbobenzyloxy (Cbz) N-protecting group conferred greater potency as a P5 site recognition unit for elastase than did dansyl, methoxysuccinyl, or tert-butyloxycarbonyl. Initial inhibition of elastase was greater when trifluoromethyl ketone 9f was added from a stock solution of dimethyl sulfoxide than when it had been buffer-equilibrated prior to assay, which suggests that the nonhydrated ketone is the more effective form of the inhibitor. The most potent elastase inhibitor we report is Na-(Ad-SO2)-N epsilon-(MeO-Suc)Lys-Pro-Val-CF3 (16) which has a Ki of 0.58 nM.
Atrial natriuretic factor elicits an endothelium-independent relaxation and activates particulate guanylate cyclase in vascular smooth muscle. (1984)

A 26 amino acid synthetic peptide fragment of atrial natriuretic factor (ANF) relaxed isolated rabbit aortic segments in which the endothelium was either intact or functionally destroyed. The relaxations were temporally associated with increases in levels of cGMP with no change in the levels of cAMP. The ANF-induced increases in cGMP were also observed in aortic segments pretreated with calcium-free buffer or the cGMP phosphodiesterase inhibitor M&B 22,948. Qualitatively similar results were obtained for sodium nitroprusside. ANF selectively activated particulate guanylate cyclase, having no effect on the soluble form of the enzyme. Thus, the direct (endothelium-independent) vasodilator effect of ANF may be mediated via increased tissue levels of cGMP. ANF appears to increase vascular cGMP levels by activation of particulate guanylate cyclase.
Algorithms for sliding block codes - An application of symbolic dynamics to information theory (1983)

Ideas which have origins in Shannon's work in information theory have arisen independently in a mathematical discipline called symbolic dynamics. These ideas have been refined and developed in recent years to a point where they yield general algorithms for constructing practical coding schemes with engineering applications. In this work we prove an extension of a coding theorem of Marcus and trace a line of mathematics from abstract topological dynamics to concrete logic network diagrams.