gebhart/patrepeval huggingface dataset:
Chip-Scale Quadrupole Mass Filters for Portable Mass Spectrometry (2010)

We report the design, fabrication, and characterization of a new class of chip-scale quadrupole mass filter (QMF). The devices are completely batch fabricated using a wafer-scale process that integrates the quadrupole electrodes, ion optics, and housing into a single monolithic block. This process eliminates the electrode-to-housing misalignments inherent in other QMFs and enables the implementation of complex device architectures. To achieve the reported integration, 1 mm × 1 mm square electrodes of heavily doped silicon were utilized, resulting in quadrupoles with an effective aperture radius of 0.707 mm and a length of 30 mm. Mass filtering was demonstrated with this unconventional device showing a mass range of 650 amu and a resolution of ~30 at a drive frequency of 1.8 MHz. When operated in the second stability region at 2.0 MHz and a mass range of 50 amu, a peak width of 0.3 amu was achieved at mass 28, showing a resolution of ~90. This paper introduces operation in the second stability region as a reliable method for turning QMFs with less than ideal electrode geometries into high-performance devices.
Counterions and the bacteriorhodopsin proton pump (1988)

Theoretical and new experimental arguments are given to explain the reversal of photoelectric signals from purple membranes oriented and immobilized in gel due to the presence of TEMED. The continuous current induced by continuous illumination demonstrates a photoelement‐like behaviour, the polarity of which is reversed by TEMED. The data render the counterion‐collapse mechanism highly questionable.
RNA Interference, Editing, and Modification (2004)

The study of RNA interference, editing, and modification has led to major shifts in our understanding of how genes are expressed and regulated. In RNA Interference, Editing, and Modification: Methods and Protocols, hands-on experimentalists describe in detail the protocols and assays they have developed to study these processes in most of the major biological systems in which they are known to occur-a wide range of organisms that includes worms, flies, trypanosomes, mammals, and plants. A historical overview of each subject is provided to put related chapters into a larger context. RNA interference (RNAi) has also emerged in recent years as an important and promising tool for gene discovery and reverse genetic engineering. Application of this cutting-edge technique is described for a range of experimental systems. Topics of interest include stable and transient RNA interference, RNA editing, gene silencing, bioinformatics, small noncoding RNAs, and RNomics.
A convenient, one-step, synthesis of β-C-glycosidic ketones in aqueous media (2000)

Condensation of pentane-2,4-dione with different unprotected sugars in alkaline aqueous media gave quantitatively in one step β-C-glycosidic ketones.
Expression of integrins and examination of their adhesive function in normal and leukemic hematopoietic cells (1993)

Adhesion of hematopoietic progenitor cells to marrow-derived adherent cells has been noted for erythroid, myeloid, and lymphoid precursors. In this report, we have characterized very late antigen (VLA) integrin expression on normal CD34+ marrow progenitors, on leukemic cell lines, and on blasts from patients with acute myelogenous or monocytic leukemias. CD34+ progenitor cells expressed the integrin beta 1 chain (CD29), VLA-4 alpha (CD49d), and VLA-5 alpha (CD49e). The myeloid lines KG1 and KG1a also expressed CD49d and CD49e as did the Mo7e megakaryoblastic line. CD29, CD18, and CD11a were also present on each of these cell lines. Only the Mo7e line expressed the cytoadhesins GPIIbIIIa or GPIb. Binding of KG1a to marrow stroma was partially inhibited by antibodies to CD49d and its ligand, vascular cell adhesion molecule (VCAM-1). The majority of leukemic blasts studied expressed CD49d and CD49e as well. Blasts from patients with acute myelomonocytic leukemia consistently bound to stroma at levels greater than 20%, and adhesion to stroma could in some cases be partly inhibited by anti-CD49d. No role for glycosylphosphatidyl-inositol (GPI)-linked structures was demonstrated in these binding assays because the adhesion of leukemic blasts to stroma was not diminished after treatment with phosphatidylinositol-specific phospholipase C (PI-PLC). These studies indicate that CD34+ myeloid progenitors, myeloid leukemic cell lines, and leukemic blasts possess a similar array of VLA integrins. Their functional importance individually or in combination with other mediators of attachment in adhesion, transendothelial migration, and differentiation has yet to be fully elucidated.
ZAP-70 binding specificity to T cell receptor tyrosine-based activation motifs: the tandem SH2 domains of ZAP-70 bind distinct tyrosine-based activation motifs with varying affinity. (1995)

Engagement of the T cell antigen receptor (TCR) results in activation of several tyrosine kinases leading to tyrosine phosphorylation of protein substrates and activation of multiple biochemical pathways. TCR-mediated activation of the src-family kinases, Lck and Fyn, results in tyrosine phosphorylation of the TCR zeta and CD3 chains. The site of phosphorylation in these chains is the tyrosine-based activation motif (TAM), a 15-16 amino acid module containing two tyrosine residues. Tyrosine-phosphorylated TAMs serve as targets for binding of the zeta-associated protein (ZAP-70) tyrosine kinase via its tandem SH2 domains. This binding correlates with activation of ZAP-70, a critical event in T cell activation. To further define the structural requirements for ZAP-70 interaction with the TCR, we developed a binding assay using immobilized glutathione S-transferase fusion proteins containing the NH2- and/or COOH-terminal SH2 domains of ZAP-70, and soluble synthetic peptides with the sequence of the cytoplasmic region of the TCR zeta chain (TCR zeta cyt) or individual TCR zeta and CD3 epsilon TAM motifs. Direct binding studies demonstrated that the tandem ZAP-70 SH2 domains bind phosphorylated, but not nonphosphorylated, TCR zeta cyt. The NH2-terminal ZAP-70 SH2 domain also binds to TCR zeta cyt but with 100-fold lower affinity. No binding was observed with the COOH-terminal ZAP-70 SH2 domain. Similar studies demonstrated that the ZAP-70 tandem SH2 domain can bind a TCR zeta 3 TAM peptide in which both tyrosine residues are phosphorylated: Little or no binding was observed with peptides phosphorylated at only one tyrosine residue, or a nonphosphorylated peptide. Binding of the tandem SH2 domains to the other two TCR zeta TAM peptides and to a CD3 epsilon TAM peptide was also observed. All four doubly tyrosine phosphorylated TAM peptides cross-compete with each other for binding to the tandem SH2 domains of ZAP-70. The affinity of these peptides for the tandem SH2 construct demonstrated a hierarchy of TAM zeta 1 > or = TAM zeta 2 > TAM epsilon > or = TAM zeta 3. The results provide further evidence that the ZAP-70 interaction with the TCR requires prior phosphorylation of both tyrosine residues within a TAM motif. Binding of ZAP-70 to phospho-TAMs is notable for the high level of cooperativity between the two SH2 domains, which individually demonstrate low affinity interaction with the ligand. The cooperativity ensures higher affinity for the doubly phosphorylated ligand. Affinity differences of as much as 30-fold indicates a significant specificity of interaction of ZAP-70 SH2 domains for different phospho-TAMs.
Immunomodulatory effects of a plasmid expressing B7‐2 on human immunodeficiency virus‐1‐specific cell‐mediated immunity induced by a plasmid encoding the viral antigen (1997)

B7 co-stimulation is essential for activating resting T cells following antigen recognition by the T cell receptor. To determine whether B7 has adjuvant activities on human immunodeficiency virus type-1 (HIV-1)-specific immunity induced by inoculation of a plasmid encoding HIV-1 env and rev (DNA vaccine), B7-1 and B7-2 expression plasmids were co-inoculated with the DNA vaccine. The delayed-type hypersensitivity response and cytotoxic T lymphocyte (CTL) activity were significantly enhanced when B7-2 expression plasmid was co-inoculated with the DNA vaccine, but were unaffected when the B7-1 expression plasmid was used with the vaccine instead. The immunological response enhanced by B7-2 decreased below the level of mice immunized with the DNA vaccine in combination with CTLA4Ig, an inhibitor of the B7/CD28 co-stimulatory signal, suggesting that this signal is critical for the enhanced response induced by co-inoculation of the DNA vaccine and B7-2 expression plasmid. This enhancement appeared to occur via an interferon-gamma (IFN-gamma)-dependent mechanism, as combined administration of the B7-2 plasmid and neutralizing anti-IFN-gamma antibody abrogated the virus-specific cell-mediated immunity. These results suggest that this gene-based co-inoculation strategy using HIV-1 viral antigen and B7-2 co-stimulatory molecule could be a powerful means of combating HIV-1 infection.
Look, Imagine and Match: Improving Textual-Visual Cross-Modal Retrieval with Generative Models (2017)

Textual-visual cross-modal retrieval has been a hot research topic in both computer vision and natural language processing communities. Learning appropriate representations for multi-modal data is crucial for the cross-modal retrieval performance. Unlike existing image-text retrieval approaches that embed image-text pairs as single feature vectors in a common representational space, we propose to incorporate generative processes into the cross-modal feature embedding, through which we are able to learn not only the global abstract features but also the local grounded features. Extensive experiments show that our framework can well match images and sentences with complex content, and achieve the state-of-the-art cross-modal retrieval results on MSCOCO dataset.
[Current screening for molecular target therapy of cancer]. (2003)

Recent progress in molecular biology and cancer biology has revealed that many molecules, which are heavily involved in the un-limited growth, anti-apoptotic effects and invasion of tumors, would be targets of cancer therapy. Part of the drugs which inhibit these molecules have shown clinical response as well as clinical benefits. In this review article, the summary of mechanism based drug screening for cancer as well as recent status of new molecular target drugs for cancer, are described.
Mapping of two loci affecting the synthesis and structure of a periplasmic protein involved in arginine and ornithine transport in Escherichia coli K-12 (1982)

The map location of two genes, abpR and abpS, was established. The abpR locus is responsible for the synthesis and the abpS locus is responsible for the structure of the arginine-ornithine-binding protein, a required component of the arginine-ornithine transport system of Escherichia coli. Two loci that result in elevated synthesis of the arginine-ornithine-binding protein and in an altered protein were mapped by bacterial conjugation and transduction studies. The mapping showed that the two genes lie in close proximity near the argA genetic marker in the order, with respect to argA, of argA abpR abpS. The maximal influx of arginine into an abpR mutant, which produces the arginine-ornithine-binding protein in an elevated amount, was substantially higher than the value obtained with an isogenic wild-type strain (apbR+). It also was observed that there was a close similarity between the affinity of the transport system for its substrate and the in vitro affinity of the binding protein for arginine both in the case of the isogenic wild type (abpS+) and a mutant (abpS6) carrying an altered protein. These results were consistent with the concept that the binding protein modulates the affinity of the transport system and suggest that it is the step of substrate recognition by the periplasmic protein which is rate-limiting in the entire process of transport at maximal influx.
Dependence of lateral oxidation rate on thickness of AlAs layer of interest as a current aperture in vertical-cavity surface-emitting laser structures (1998)

The dependence of the wet oxidation process on the AlAs layer thickness used in selectively oxidized vertical-cavity surface-emitting-laser structures is studied in detail. A theoretical model based on a diffusion-reaction process is proposed. A rapid reduction in the oxidation rate is predicted with a reduction in the layer thickness of the ultrathin AlAs layer. The theoretical predictions are verified through experiments.
Effects of intracoronary infusion of arterial blood or Fluosol-DA 20% on regional myocardial metabolism and function during brief coronary artery occlusions. (1987)

Effects of intracoronary infusion (50 ml/min) of arterial blood, oxygenated or unoxygenated Fluosol, or Plasmalyte A on hemodynamics, electrocardiogram, regional myocardial function, and lactate metabolism were studied in six closed-chest dogs during 2 min occlusions of the left anterior descending coronary artery followed by 10 min of reperfusion. Normal hemodynamics were maintained with infusion of arterial blood and oxygenated Fluosol, whereas unoxygenated Fluosol and Plasmalyte A resulted in hemodynamic deterioration similar to that noted with no treatment. Ischemic zone systolic fractional area change, an index of systolic function measured by two-dimensional echocardiography, remained normal during the occlusion supplemented with intracoronary arterial blood (49 +/- 7%), was moderately hypokinetic with oxygenated Fluosol (31 +/- 10%), and became severely hypokinetic with unoxygenated Fluosol (14 +/- 14%), with Plasmalyte A (2 +/- 13%), and in the absence of treatment (5 +/- 9%). Only infusion of arterial blood resulted in no ST segment elevation or lactate production. Thus intracoronary infusion of arterial blood during brief coronary occlusion maintained normal myocardial function and aerobic metabolism. Infusion of oxygenated Fluosol resulted in amelioration of the decline in regional function after coronary occlusion, but not complete protection.
Relative affine structure: canonical model for 3D from 2D geometry and applications (1996)

We propose an affine framework for perspective views, captured by a single extremely simple equation based on a viewer-centered invariant we call relative affine structure. Via a number of corollaries of our main results we show that our framework unifies previous work-including Euclidean, projective and affine-in a natural and simple way, and introduces new, extremely simple algorithms for the tasks of reconstruction from multiple views, recognition by alignment, and certain image coding applications.
BIOLOGICAL ACTION OF 17?-HYDROXYPROGESTERONE 17-n-CAPROATE ON THE REPRODUCTIVE PROCESSES OF THE RAT (1958)

The effect of Detalutin on estrous cycles mating ovulation and implantation estradiol-17beta-induced uterine growth and litter size in albino rats was studied. .5-7.5 mg Delalutin daily for 7 days for 3 cycles did not delay estrous cycles; it decreased the variability of the rat estrous cycle. Progesterone pretreatment delayed mating time while Delalutin pretreatment caused mating to occur in about 1/3 the control time. The number of corpora lutea and implantations was also highest with Delalutin. Delalutin did not significantly inhibit the uterine-growth-inducing action of estradiol-17-beta not did it suppress the number of living young per litter as progesterone did. No females treated with Delalutin aborted.
Rheological Properties of Several Hyaluronic Acid-Based Gels: A Comparative Study. (2018)

Adding lidocaine to HA gels does modify their rheological properties yet this, to a variable extent depending on the product. J Drugs Dermatol. 2018;17(9):948-954.
Iridium(III)-Catalyzed Regioselective C7-Amination of N-Pivaloylindoles with Sulfonoazides (2016)

Direct C7-amination of N-pivaloylindoles has been achieved using a combination of [Cp*IrCl<sub>2</sub>]<sub>2</sub>, AgNTf<sub>2</sub>, and AgOAc as the catalyst and sulfonoazides as the nitrogen source. The reaction proceeded at room temperature to 80 °C to afford 7-sulfonamidoindoles in good to excellent yields. The reaction is broadly applicable to the C7-amination of a wide variety of 3-, 4-, 5-, and 6-substituted N-pivaloylindoles with either alkyl or aryl sulfonoazides.
Efficient expression of retroviral vector-transduced human low density lipoprotein (LDL) receptor in LDL receptor-deficient rabbit fibroblasts in vitro. (1988)

Familial hypercholesterolemia is caused by a genetic deficiency of the low density lipoprotein (LDL) receptor. The Watanabe heritable hyperlipidemic (WHHL) rabbit, which is also defective in LDL receptor activity, provides an excellent animal model of homozygous familial hypercholesterolemia. As a step toward development of effective gene therapy for familial hypercholesterolemia, we have constructed a transmissible retroviral vector containing a full-length human cDNA for the LDL receptor. WHHL fibroblasts infected in vitro expressed the human receptor efficiently, as indicated by RNA and ligand blotting studies. Infected fibroblasts bound and degraded a monoclonal antibody specific for the human LDL receptor (IgGC7) in a manner comparable to that seen with normal human fibroblasts. Human LDL was also degraded by infected WHHL cells and promoted cholesterol esterification to the same degree as seen in normal human fibroblasts. Although technical problems remain to be solved, these studies show that, in principle, gene therapy may be possible for familial hypercholesterolemia patients.
Inhibition of angiogenesis through modulation of collagen metabolism. (1988)

Combinations of angiostatic steroids and heparin induce basement membrane breakdown, capillary retraction, and endothelial cell rounding as part of their antiangiogenic action (Ingber DE, Madri JA, Folkman J: Endocrinology 119:1768, 1986). Specific modulators of matrix metabolism were examined for their effects and on capillary development in the growing chick chorioallantoic membrane to explore the possibility that structural alterations of extracellular matrix (ECM) could be causally involved in the antiangiogenic mechanism. Regression of growing capillaries was induced by proline analogs (1-azetidine-2-carboxylic acid, cis-hydroxyproline,d,L-3,4-dehydroproline, thioproline) and an inhibitor of prolyl hydroxylase (alpha,alpha-dipyridyl) which interfere with triple helix formation and prevent collagen deposition. Beta-aminopropionitrile, an inhibitor of collagen cross-linking, was also antiangiogenic although an inhibitor of glycosaminoglycan deposition (beta-methyl d-xyloside) was not. Combination of suboptimal doses of active collagen modulators with either angiostatic steroids or heparin resulted in great potentiation of their antiangiogenic effects. Coadministration of proline analogs, angiostatic steroids, and heparin resulted in complete inhibition of angiogenesis (avascular zones in 100% of chorioallantoic membranes) and larger and more extensive avascular zones than previously observed with steroid-heparin combinations. The antiangiogenic effects of these compounds (alone and in combination) were found to be directly related to their ability to inhibit collagen accumulation. Screening of additional compounds that are known to alter ECM turnover resulted in identification of a new angiogenesis inhibitor, all trans-retinoic acid. These findings suggest that growing capillaries may be "switched" into a regressive mode through alterations of collagen metabolism that result in loss of ECM structural integrity. Identification of ECM turnover as a major control point in angiogenesis may also provide a more rational approach for development of new antiangiogenic regimens.
Inhibition by sumatriptan of central trigeminal neurones only after blood‐brain barrier disruption (1993)

1. The 5-hydroxytryptamine (5-HT1)-like agonist, sumatriptan, is highly efficient in the relief of migraine headache and its accompanying symptoms. 2. Experimental evidence has indicated that its site of action may be on the cranial vessels or on the trigeminal innervation of the cranium, or both, since sumatriptan does not pass the blood-brain barrier easily under normal circumstances. It is, however, not clear whether the blood-brain barrier is normal or abnormal during a migraine attack. 3. In this study, single unit activity and trigeminal somatosensory evoked potentials in central trigeminal neurones were monitored during electrical stimulation of the superior sagittal sinus. 4. Intravenous administration of sumatriptan (100 micrograms kg-1) did not alter trigeminal evoked activity unless the permeability of the blood-brain barrier had been increased by infusion of an hyperosmolar mannitol solution. After blood-brain barrier disruption, sumatriptan decreased the peak-to-peak amplitude of evoked potentials by 40 +/- 6% and the probability of firing of single units by 30 +/- 9%. Mannitol infusions alone in control animals caused no changes in evoked potentials or single unit activity. 5. The data suggest that in normal circumstances sumatriptan does not have sufficient access to trigeminal neurons to alter their function.
Eradication of spontaneous malignancy by local immunotherapy (2018)

It has recently become apparent that the immune system can cure cancer. In some of these strategies, the antigen targets are preidentified and therapies are custom-made against these targets. In others, antibodies are used to remove the brakes of the immune system, allowing preexisting T cells to attack cancer cells. We have used another noncustomized approach called in situ vaccination. Immunoenhancing agents are injected locally into one site of tumor, thereby triggering a T cell immune response locally that then attacks cancer throughout the body. We have used a screening strategy in which the same syngeneic tumor is implanted at two separate sites in the body. One tumor is then injected with the test agents, and the resulting immune response is detected by the regression of the distant, untreated tumor. Using this assay, the combination of unmethylated CG-enriched oligodeoxynucleotide (CpG)-a Toll-like receptor 9 (TLR9) ligand-and anti-OX40 antibody provided the most impressive results. TLRs are components of the innate immune system that recognize molecular patterns on pathogens. Low doses of CpG injected into a tumor induce the expression of OX40 on CD4<sup>+</sup> T cells in the microenvironment in mouse or human tumors. An agonistic anti-OX40 antibody can then trigger a T cell immune response, which is specific to the antigens of the injected tumor. Remarkably, this combination of a TLR ligand and an anti-OX40 antibody can cure multiple types of cancer and prevent spontaneous genetically driven cancers.