gebhart/patrepeval huggingface dataset:
Solid-Phase Synthesis of 5-Isoxazol-4-yl-[1,2,4]oxadiazoles (2004)

A library of isoxazole and 1,2,4-oxadiazole-containing diheterocyclic compounds has been prepared. Our strategy was explored in solution phase first as follows. PMB-protected 3-butyn-2-ol was deprotonated with nBuLi, acylated with methyl chloroformate, and then employed in a nitrile oxide 1,3-dipolar cycloaddition (benzaldehyde oxime in the presence of bleach) to afford the isoxazole-substituted carboxylic acid methyl ester. Ester saponification with aqueous NaOH followed by a two-step condensation with benzamidoxime gave the final isoxazole-oxadiazole diheterocyclic product in good yield. With some modifications, we next explored this chemistry on Wang resin, which led to 18 final products that were cleaved from polymer beads with 50% TFA in dichloromethane.
Design and Evaluation of a Human Immunodeficiency Virus Type 1 RNA Assay Using Nucleic Acid Sequence-Based Amplification Technology Able To Quantify Both Group M and O Viruses by Using the Long Terminal Repeat as Target (1999)

Currently available human immunodeficiency virus type 1 (HIV-1) RNA quantification assays can detect most viruses of the group M subtypes, but a substantial number are missed or not quantified reliably. Viruses of HIV-1 group O cannot be detected by any commercially available assay. We developed and evaluated a quantitative assay based on nucleic acid sequence-based amplification (NASBA) technology, with primers and probes located in the conserved long terminal repeat (LTR) region of the HIV-1 genome. In 68 of 72 serum samples from individuals infected with HIV-1 subtypes A to H of group M, viruses could be detected and quantified. In serum samples from two patients infected with HIV-1 group O viruses, these viruses as well could be detected and quantified. In contrast, the currently used gag-based assay underestimated the presence of subtype A viruses and could not detect subtype G and group O viruses. The discrepancy between the results of the two assays may be explained by the number of mismatches found within and among the probe and primer regions of the subtype isolates. These data indicate that LTR-based assays, including the NASBA format chosen here, are better suited to monitoring HIV-1 therapy than are gag-based assays in an era in which multiple HIV-1 subtypes and groups are spreading worldwide.
Effective treatment of metastatic MDA-MB-435 human estrogen-independent breast carcinomas with a targeted cytotoxic analogue of luteinizing hormone-releasing hormone AN-207. (2000)

A highly potent derivative of doxorubicin, 2-pyrrolinodoxorubicin (AN-201), was linked to [D-Lys6]luteinizing hormone-releasing hormone (LH-RH) to form a cytotoxic analogue, AN-207, that can be targeted to LH-RH receptors. The effects of AN-207 were investigated in MDA-MB-435 human estrogen-independent breast carcinomas, which express LH-RH receptors. In experiment 1, nude mice bearing orthotopically implanted tumors received a single i.v. injection of AN-207, AN-201, or the carrier at 250 nmol/kg. Five weeks after administration of AN-207, tumor volume was significantly decreased by 66% (P < 0.001) and tumor burden by 71% (P < 0.05) as compared with controls, but no significant effects occurred in other groups. Six of eight (75%) control animals and 37.5% of mice treated with AN-201 developed metastases in the lymph nodes, whereas no lymphatic spread was found in any of the mice that received injections of AN-207. The antitumor effect of AN-207 could be partially blocked by pretreatment of the tumor-bearing mice with high doses of agonist [D-Trp6]LH-RH, which suggests that AN-207 acts on LH-RH receptors on tumors. The mortality due to toxicity was 25% in the group receiving AN-201 and 12.5% in the AN-207-treated group. Radioligand binding assays revealed the presence of high-affinity binding sites for LH-RH on tumor membranes, and mRNA for LH-RH receptors was demonstrated by reverse transcription-PCR. In experiment 2, two i.v. injections of AN-207 or AN-201 at 150 nmol/kg were given on days 0 and 28 to mice bearing orthotopic xenografts of MDA-MB-435. The outcome of the treatment was similar to that observed in experiment 1, but without any toxicity-related deaths. Tumor growth inhibition and prevention of metastatic disease suggest that cytotoxic LH-RH analogue AN-207 could be considered for the treatment of human estrogen-independent breast cancers expressing receptors for LH-RH.
Migration-stimulating factor: a genetically truncated onco-fetal fibronectin isoform expressed by carcinoma and tumor-associated stromal cells. (2003)

Migration-stimulating factor (MSF) is a 70-kDa motogenic protein previously reported to be expressed by fetal and cancer patient fibroblasts cultured in vitro and present in the serum of breast cancer patients. A 2.2-kb full-length MSF cDNA has been cloned and shown to be a truncated isoform of fibronectin generated from its primary gene transcript by a hitherto unrecognized intron read-through mechanism. MSF cDNA is identical to the 5' end of fibronectin cDNA, up to and including exon III-1a, and terminates in a novel 195-nucleotide 3' sequence. This MSF unique sequence is derived from the intron immediately downstream of exon III-1a in the fibronectin gene and is not found in any previously identified "full-length" fibronectin cDNA. MSF mRNA is 1000-fold less abundant than full-length fibronectin message in fetal fibroblasts and exhibits rapid biphasic decay kinetics previously associated with oncogenes and stress response molecules. MSF recombinant protein exhibits a potent and substratum-dependent motogenic activity, with half-maximal response manifest at 0.1-1.0 pg/ml. This activity is (a) mediated by the IGD amino acid motif; and (b) not expressed by (i.e., cryptic within) full-length fibronectin. In situ hybridization and immunohistochemistry confirm that MSF is expressed by tumor-associated fibroblasts and additionally indicate that it is also expressed by carcinoma cells and tumor-associated vascular endothelial cells. MSF, as a consequence of its potent bioactivities and expression by both stromal and carcinoma cell populations, is well placed to function as an epigenetic effector promoting cancer development.
Molecular Mechanisms and Biological Significance of CTL Avidity (2003)

CD8 CTLs are a major effector for protection against cancer as well as many infectious diseases, including HIV/AIDS. CD8 CTL recognize antigenic peptides in the context of class I MHC. CTL functional avidity has been shown to be an important determinant of in vivo efficacy. CTL that can recognize peptide/MHC only at high antigen density are termed low avidity CTL, while those that can recognize their cognate antigen at low densities are termed high avidity CTL. Recent studies have demonstrated that high avidity CTLs are essential for the effective clearance of viral infections and for the elimination of tumor cells. At this time, approaches that can target high avidity cells for expansion in vivo are not well defined; however, new insights are beginning to emerge. A recent study has shown that prime-boost immunization may be an effective method to generate high avidity CTLs that recognize HIV antigens. In addition, we recently found that high levels of costimulation (signal 2) can skew the CTL response toward higher avidity cells. Thus, vectors expressing a triad of costimulatory molecules (TRICOM) or dendritic cells expressing higher levels of costimulatory molecules, can be used to induce high avidity CTL. Finally a critical role for CD4+ T cell help in the generation of high avidity cells has recently been identified (Palmer, manuscript submitted). While high avidity CTLs are superior for viral and tumor clearance, they also have a greater sensitivity to antigen induced cell death. In some types of chronic infections, such as HIV and HCV, as well as in cancer, the host may lose, by clonal exhaustion or other apoptotic mechanisms, the effector cells that are most critical to viral or tumor clearance. In this review, we examine the current knowledge concerning CTL avidity. We discuss the factors that may distinguish high avidity CTLs from low avidity CTLs and describe some of the mechanisms these cells use to clear viral infections. In addition, we study possible immunization strategies that may be used to elicit higher avidity CTLs and describe what is known about the factors that render these cells more susceptible to apoptosis than low avidity CTLs. Finally, we will incorporate these various elements into a general discussion of possible approaches for induction and maintenance of an effective immune response that can result in clearance of tumors or chronic viral infections and the relevance to vaccine development.
In Vivo Gene Transfer to Mouse Spermatogenic Cells by Deoxyribonucleic Acid Injection into Seminiferous Tubules and Subsequent Electroporation1 (1998)

An in vivo gene transfer technique for living mouse testes was used to develop a novel transient expression assay system for transcriptional regulatory elements of spermatogenic specific genes. The combination of DNA injection into seminiferous tubules and subsequent in vivo electroporation resulted in an efficient and convenient assay system for gene expression during spermatogenesis. The transfer of the firefly luciferase reporting gene driven by the Protamine-1 (Prm-1) enhancer region revealed a significant increase in the activity of the reporter enzyme. Histochemical studies of the transfer of the lacZ gene driven by the Prm-1 enhancer showed specific lacZ expression only in haploid spermatid cells in adult testes, corresponding with the expression pattern of endogenous Prm-1. We were able to detect long-lasting transgene expression in the transfected spermatogenic cells. A group of spermatogenic differentiating cells maintained the transfected lacZ expression after more than 2 mo of transfection, suggesting that spermatogenic stem cells and/or spermatogonia could also incorporate foreign DNA and that the transgene could be transmitted to the progenitor cells derived from a transfected proliferating germ cell.
A Green-emitting Fluorescent Protein from Galaxeidae Coral and Its Monomeric Version for Use in Fluorescent Labeling (2003)

We have cloned a gene which encodes a fluorescent protein from the stony coral, Galaxeidae. This protein absorbs light maximally at 492 nm and emits green light at 505 nm, and as a result, we have designated it "Azami-Green (AG)." Despite sharing a similar spectral profile with enhanced green fluorescent protein (EGFP) (Clontech), the most popular variant of the Aequorea victoria green fluorescent protein, the identity between these two proteins at the amino acid level is only 5.7%. However, since AG has a high extinction coefficient, fluorescence quantum yield, and acid stability, it produces brighter green fluorescence in cultured cells than EGFP. Similar to other fluorescent proteins isolated from coral animals, AG forms a tight tetrameric complex, resulting in poor labeling of subcellular structures such as the plasma membrane and mitochondria. We have converted tetrameric AG into a monomeric form by the introduction of three amino acid substitutions, which were recently reported to be effective for monomerizing the red fluorescent protein from Discosoma coral (DsRed, Clontech). The resultant monomeric AG allowed for efficient fluorescent labeling of all of the subcellular structures and proteins tested while retaining nearly all of the brightness of the original tetrameric form. Thus, monomeric AG is a useful monomeric green-emitting fluorescent protein comparable to EGFP.
Siamese Neural Networks for One-shot Image Recognition (2015)

The process of learning good features for machine learning applications can be very computationally expensive and may prove difficult in cases where little data is available. A prototypical example of this is the one-shot learning setting, in which we must correctly make predictions given only a single example of each new class. In this paper, we explore a method for learning siamese neural networks which employ a unique structure to naturally rank similarity between inputs. Once a network has been tuned, we can then capitalize on powerful discriminative features to generalize the predictive power of the network not just to new data, but to entirely new classes from unknown distributions. Using a convolutional architecture, we are able to achieve strong results which exceed those of other deep learning models with near state-of-the-art performance on one-shot classification tasks.
Low-dimensional nanomaterial saturable absorbers for ultrashort-pulsed waveguide lasers (2018)

A wide range of saturable absorbers composed of novel low-dimensional nanomaterials were fabricated, and their linear and nonlinear optical properties were characterized. Furthermore, their suitability for ultrashort-pulse generation in waveguide laser operating at a wavelength of 2 microns was demonstrated and passively q-switched mode-locked operation was achieved with all absorbers. The material systems that were studied in this work include nanosheet-based absorbers composed of graphene, carbon nanotubes, black phosphorus, transition-metal dichalcogenides, topological insulators and indium tin oxide. By utilizing a uniform few-layer spin coating fabrication technique and by employing a single, identical laser resonator, a direct comparison of the individual characteristics of these materials in the context of short-pulse generation in waveguide lasers was made possible. Each of the individually fabricated and characterized saturable absorbers was placed inside a thulium-doped fluoride glass waveguide chip laser cavity and the resulting output performance was analyzed and contrasted. It was further found that the few-layer spin coating approach enables fine-tuning of the absorber characteristics and that all low-dimensional nanomaterials under investigation can be utilized for ultrashort pulse generation in the 2-micron wavelength range. General guidelines for the design of passively modulated short-pulsed laser oscillators are presented based on those findings.
Analysis of antigenic domains on natural and recombinant human IFN- beta by the inhibition of biologic activities with monoclonal antibodies. (1989)

Human IFN-beta (HuIFN-beta) is a biologically potent protein with both antiviral and antiproliferative activities. To understand better its mode of action, a number of murine mAb were developed against a recombinant (serine-17) HuIFN-beta (rHuIFN-beta ser) and screened by ELISA and neutralization of antiviral activity. The panel of antibodies, composed of both IgA and IgG immunoglobulins, were specific for HuIFN-beta and did not crossreact with HuIFN-alpha or gamma. Furthermore, three functionally distinct epitopes (designated as sites I, II, and III) were identified based on mAb neutralization of antiviral and antiproliferative activities of recombinant and natural HuIFN-beta. Antibodies directed to sites I and II neutralized the antiviral and antiproliferative activities of rHuIFN-beta ser, though the antiviral neutralization potency of the mAb to site II was approximately 10-fold less than mAb to site I. Antibodies directed to site I neutralized both recombinant and natural HuIFN-beta, although the antiviral neutralization potency was approximately 10-fold higher against rHuIFN-beta ser than the native protein. The mAb directed to site II did not demonstrate any significant neutralization of the antiviral or antiproliferative activity of natural HuIFN-beta but neutralized a recombinant HuIFN-beta containing the native sequence. Antibodies recognizing site III did not neutralize the biologic activity of either recombinant or natural HuIFN-beta. Thus, three epitopes on HuIFN-beta have been identified, two of which are associated with both antiviral and antiproliferative activities.
Deep Neural Networks Segment Neuronal Membranes in Electron Microscopy Images (2012)

We address a central problem of neuroanatomy, namely, the automatic segmentation of neuronal structures depicted in stacks of electron microscopy (EM) images. This is necessary to efficiently map 3D brain structure and connectivity. To segment biological neuron membranes, we use a special type of deep artificial neural network as a pixel classifier. The label of each pixel (membrane or non-membrane) is predicted from raw pixel values in a square window centered on it. The input layer maps each window pixel to a neuron. It is followed by a succession of convolutional and max-pooling layers which preserve 2D information and extract features with increasing levels of abstraction. The output layer produces a calibrated probability for each class. The classifier is trained by plain gradient descent on a 512 × 512 × 30 stack with known ground truth, and tested on a stack of the same size (ground truth unknown to the authors) by the organizers of the ISBI 2012 EM Segmentation Challenge. Even without problem-specific postprocessing, our approach outperforms competing techniques by a large margin in all three considered metrics, i.e. rand error, warping error and pixel error. For pixel error, our approach is the only one outperforming a second human observer.
Integrating virtual and augmented realities in an outdoor application (2003)

This paper explores interconnecting outdoor AR systems with a VR system to achieve collaboration in both domains simultaneously. We envisage multiple mobile users of wearable AR systems interacting with a stationary VR facility via a wireless network. An application in simulated combat training is described, where the AR users are soldiers with wearable computers, and the VR system is located at a command and control centre. For soldiers, AR provides enhanced information about the battlefield environment, which may include the positions and attributes of simulated entities for the purpose of training outdoors at low cost. At the same time a complete picture of the battlefield, including real and simulated troops and vehicles, is available via the VR system. As soldiers move about, their GPS and digital compass hardware provide the remote VR user and other AR users with the means to track their position in real-time. We describe a working system based on our modular Tinmith-II wearable computer, which interacts with a combat simulator to create a synthetic battle environment for safe training and monitoring.
Guidelines simplify well test interpretation (1994)

With a few simple guidelines, industry professionals, especially those who are not well-testing experts, can know more about well-test interpretation, and thus make more appropriate decisions for well tests. Today's well tests frequently provide much more than permeability, skin, and extrapolated pressure. Most managers, geoscientists, and petroleum engineers rely on specialists to interpret pressure-transient data from well tests. At times, however, valuable test results are overlooked when modern analysis techniques are not used to interpret the acquired data. The first in a series of three articles addresses what to expect from a well test interpretation. The second part will show how to design a test, and manage well site data acquisition to ensure optimum results. The concluding part will illustrate these concepts in two successful cases.
Thieno[3,2-d]pyrimidines. Part-I. Preparation and Antimicrobial Activity of 3-N-Substituted-thioureido-2-methyl-6-phenylthieno[3,2-d]pyrimidin-4(3H)-ones (1997)

Department of Chemistry. Saurashtra Universitty, Rajlot-360 005 <em>Manuscript received 21 December 1994. revised 5 July 1995, accepted 26 July 1995</em> Thieno[3,2-<em>d</em>]pyrimidines. Part-I. Preparation and Antimicrobial Activity of 3-<em>N</em>-Substituted-thioureido-2-methyl-6-phenylthieno[3,2-<em>d</em>]pyrimidin-4(3<em>H</em>)-ones.
Discourse Structure and Discourse Interpretation (1997)

Proceedings of the Twenty-Third Annual Meeting of the Berkeley Linguistics Society: General Session and Parasession on Pragmatics and Grammatical Structure (1997)
Xenopus oocyte germinal-vesicle breakdown induced by [Val12]Ras is inhibited by a cytosol-localized Ras mutant. (1989)

The GTPase-activating protein (GAP) has been postulated to function either as a negative regulator or as a possible target protein of Ras in mammalian cells and Xenopus oocytes. Ras must be localized in the plasma membrane of vertebrate cells to function, but GAP is localized in the cytosol. To test whether Ras function depends on a cytosolic factor such as GAP, we microinjected into Xenopus oocytes a form of Saccharomyces cerevisiae RAS1 ([Leu68]RAS1 terminated at residue 185, called [Leu68]RAS1(term.] that lacks the consensus membrane localization site, does not respond to GAP in a GTPase assay, but binds to GAP 100-fold more tightly than [Val12]Ras. [Leu68]RAS1(term.) alone did not stimulate oocyte germinal-vesicle breakdown. Instead, [Leu68]RAS1(term.) was observed to inhibit the action of insulin-like growth factor 1 or microinjected [Val12]Ras but not the action of progesterone as monitored by germinal-vesicle breakdown. Coinjection of purified mammalian GAP with [Leu68]RAS1(term.) reduced the inhibition of [Val12]Ras-stimulated germinal-vesicle breakdown. The results raise the possibility that a cytosolic factor is required for the action of [Val12]Ras in Xenopus oocytes and that this factor is either GAP or another protein with which GAP can compete for binding to [Leu68]RAS1(term.).
Protection by dimethylthiourea against retinal light damage in rats. (1992)

The protective effect of dimethylthiourea (DMTU) against retinal light damage was determined in albino rats reared in darkness or in weak cyclic light. Rats maintained under these conditions were treated with DMTU at different concentrations and dosing schedules and then exposed for various times to intense visible light, either intermittently (1 hr light and 2 hr dark) or continuously. The extent of retinal light damage was determined 2 weeks after light exposure by comparing rhodopsin levels in experimental rats with those in unexposed control animals. To determine the effect of DMTU on rod outer segment (ROS) membrane fatty acids, ROS were isolated immediately after intermittent light exposure, and fatty acid compositions were measured. The time course for DMTU uptake and its distribution in serum, retina, and the retinal pigment epithelium (RPE)/choroid complex was determined in other rats not exposed to intense light. After intraperitoneal injection of the drug (500 mg/kg body weight), DMTU appeared rapidly in the serum, retina, and the RPE and choroid. In the ocular tissues, it was distributed 70-80% in the retina and 20-30% in the RPE and choroid. This antioxidant appears to have a long half-life because it was present in these same tissues 72 hr after a second intraperitoneal injection. For rats reared in the weak cyclic light environment, DMTU (two injections) provided complete protection against rhodopsin loss after intense light exposures of up to 16 hr. Only 15% rhodopsin loss was found in cyclic-light DMTU-treated rats after 24 hr of intermittent or continuous light. For rats reared in darkness, DMTU treatment resulted in a rhodopsin loss of less than 20% after 8-16 hr of continuous light and approximately 40% after similar exposure to intermittent light. Irrespective of the type of light exposure, rhodopsin loss in the dark-reared DMTU-treated rats was nearly identical to that found in uninjected cyclic light-reared animals. In rats from both light-rearing environments, DMTU treatment prevented the light-induced loss of docosahexaenoic acid from ROS membranes. As measured by rhodopsin levels 2 weeks later, DMTU was most effective when given as two doses administered 24 hr before and just before intense light exposure. As a single dose given during continuous light exposure, DMTU protected cyclic light-reared rats for at least 4 hr after the start of exposure but was ineffective in dark-reared animals if injected 1 hr after the start of light. It was also ineffective in both types of rats when given after light exposure.(ABSTRACT TRUNCATED AT 400 WORDS)