gebhart/patrepeval huggingface dataset:
Yeast as a tool for characterizing mono-ADP-ribosyltransferase toxins (2009)

The emergence of bacterial antibiotic resistance poses a significant challenge in the pursuit of novel therapeutics, making new strategies for drug discovery imperative. We have developed a yeast growth-defect phenotypic screen to help solve this current dilemma. This approach facilitates the identification and characterization of a new diphtheria toxin (DT) group, ADP-ribosyltransferase toxins from pathogenic bacteria. In addition, this assay utilizes Saccharomyces cerevisiae, a reliable model for bacterial toxin expression, to streamline the identification and characterization of new inhibitors against this group of bacterial toxins that may be useful for antimicrobial therapies. We show that a mutant of the elongation factor 2 target protein in yeast, G701R, confers resistance to all DT group toxins and recovers the growth-defect phenotype in yeast. We also demonstrate the ability of a potent small-molecule toxin inhibitor, 1,8-naphthalimide (NAP), to alleviate the growth defect caused by toxin expression in yeast. Moreover, we determined the crystal structure of the NAP inhibitor-toxin complex at near-atomic resolution to provide insight into the inhibitory mechanism. Finally, the NAP inhibitor shows therapeutic protective effects against toxin invasion of mammalian cells, including human lung cells.
[Transformation by SV 40 virus sensitizes fibroblasts of human skin to the lytic action of H-1 parvovirus]. (1985)

Human skin fibroblasts which are naturally resistant to Parvovirus H-1 can be lysed by this virus after SV40 transformation. This observation raises the possibility that oncosuppression by Parvovirus involves a direct oncolytic effect.
Optical resonators with whispering-gallery modes-part I: basics (2006)

We briefly review basic properties of dielectric whispering gallery mode resonators that are important for applications of the resonators in optics and photonics.
Fluorescence Monitoring of Rapid Cycle PCR for Quantification (1998)

The polymerase chain reaction (PCR) benefits from rapid temperature cycling (Wittwer et al., 1994). In particular, rapid cycling appears to improve the quantitative PCR of rare transcripts (Tan and Weis, 1992). The glass capillaries used as sample containers for rapid cycling are natural cuvettes for fluorescence analysis. Fluorometric monitoring of PCR has been reported with double-stranded DNA (dsDNA) dyes (Higuchi et al., 1992; Higuchi et al., 1993; Ishiguro et al., 1995; Wittwer et al., 1997a) and sequence-specific probes (Lee et al., 1993; Livak et al., 1995; Wittwer et al., 1997a). We have integrated a fluorimeter with a rapid temperature cycler for fluorescence monitoring during amplification (Wittwer et al., 1997b). Both cycle-by-cycle fluorescence monitoring and continuous (within cycle) monitoring offer unique quantitative information.
A survey of Hammett substituent constants and resonance and field parameters (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA survey of Hammett substituent constants and resonance and field parametersCorwin. Hansch, A. Leo, and R. W. TaftCite this: Chem. Rev. 1991, 91, 2, 165–195Publication Date (Print):March 1, 1991Publication History Published online1 May 2002Published inissue 1 March 1991https://pubs.acs.org/doi/10.1021/cr00002a004https://doi.org/10.1021/cr00002a004research-articleACS PublicationsRequest reuse permissionsArticle Views63411Altmetric-Citations7091LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Aloe Verain the Treatment of Radiation Ulcers of Mucous Membranes (1939)

IN 1935, Collins and Collins (1) published a favorable report on the treatment of roentgen dermatitis with the fresh whole leaf of Aloe vera. Later that year Collins (2) added a report on the use of an ointment of Aloe vera (Alvagel) as a therapeutic agent for roentgen and radium burns. The following year Wright (5) gave a paper on the use of Aloe vera in the treatment of roentgen ulcers and telangiectasis. He concluded that (5): “From the cases reported it would seem that x-ray ulceration, even of several years' duration, will respond to the use of Aloe vera. The permanence of the results can be determined only by watching cases thus treated over a period of time. Little can be expected in the treatment of telangiectasis as a result of irradiation beyond the smoothing and softening of the affected skin.” Probably the most recent and authoritative information, worth quoting at length to bring it to the attention of radiologists, comes from MacKee, who says (3): “During the past two or three years excellent results have been obtained with the jelly obtained from the leaf of a plant called Aloe vera. The plant grows in Florida. The leaf is green in color and long and wide—somewhat like a sword. The shell of the leaf is thick and tough, but when fresh can be cut easily with a knife. On one side of the leaf the shell is flat; on the other side it is convex. There is a thick layer of jelly-like substance between the shells. The leaf should be kept in a cool, moist environment. It is customary to cut a piece of the leaf to the size and shape of the lesion. The convex shell layer is removed. The jelly is placed in contact with the floor of the ulcer and held in place with a bandage. Dressings are changed once or twice daily. The treatment seems to be inefficacious for roentgen or radium sequelæ—atrophy, telangiectasia, sclerosis, and keratosis. It appears most effective in the case of indolent roentgen and radium ulcers. Often the pain disappears within a day or two and healing takes place in a few weeks or a few months—more often the latter. The writer can vouch for the good results in a fairly large percentage of indolent ulcers. Good results have been obtained also in ulcers that occur early in third-degree reactions. “To obtain satisfactory results it seems necessary to use the fresh leaf. Preparations on the market which contain the Aloe vera jelly have been thus far unsatisfactory. It is thought that the good results are due to vitamin D.” Our own personal experience in man has been limited to five cases. All five have experienced definite relief from pain and discomfort, as mentioned by MacKee. One case of severe roentgen dermatitis of the face, treated two years ago with the fresh leaf, can be recorded as an excellent result.
Development of a real time monitoring and adaptive control system for laser flame cutting (2009)

A real-time, adaptive control and optimization system for laser flame cutting of thick plates of mild steel has been developed. The proposed system consists of two subsystems: a process monitoring system and a control and optimization system. The first subsystem aims at the on-line observation of the process status and corresponding cut quality. Since the different cut quality characteristics (e.g. cutting edge striations or dross) cannot be measured directly, the proposed system is based on so-called sensing parameters, which are easily-observable physical parameters that correlate well with the quality characteristics of the cut surface. The applicability of different optical sensors (photodiodes and a NIR-camera) has been investigated. The most optimal configuration of the process monitoring system is presented, including an overview of the selected set of sensing parameters. The second subsystem, the real-time control and optimization system, supports the adaptation of the process parameters, based on the cut quality information obtained from the process monitoring system. A suitable hardware configuration for the real-time control and optimization is presented, starting from the original platform (i.e. an industrial 2D laser cutting machine). A generic expert strategy, has been designed for the control and optimization purpose. Using the developed experimental platform, the performance of the expert system was verified and optimized for different material-thickness combinations. The obtained results demonstrate the effectiveness of the chosen approach in terms of increased autonomy, productivity, and efficiency of the process, as well as elimination of the need for manual quality control and the possibility to automatically generate quality reports.
Novel analogs of nucleoside 3',5'-cyclic phosphates. I. 5'-Mono- and dimethyl analogs of adenosine 3',5'-cyclic phosphate (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNovel analogs of nucleoside 3',5'-cyclic phosphates. I. 5'-Mono- and dimethyl analogs of adenosine 3',5'-cyclic phosphateR. Ranganathan, G. H. Jones, and J. G. MoffattCite this: J. Org. Chem. 1974, 39, 3, 290–298Publication Date (Print):February 1, 1974Publication History Published online1 May 2002Published inissue 1 February 1974https://pubs.acs.org/doi/10.1021/jo00917a003https://doi.org/10.1021/jo00917a003research-articleACS PublicationsRequest reuse permissionsArticle Views650Altmetric-Citations75LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
TLR9-mediated siRNA delivery for targeting of normal and malignant human hematopoietic cells in vivo (2013)

STAT3 operates in both cancer cells and tumor-associated immune cells to promote cancer progression. As a transcription factor, it is a highly desirable but difficult target for pharmacologic inhibition. We have recently shown that the TLR9 agonists CpG oligonucleotides can be used for targeted siRNA delivery to mouse immune cells. In the present study, we demonstrate that a similar strategy allows for targeted gene silencing in both normal and malignant human TLR9(+) hematopoietic cells in vivo. We have developed new human cell-specific CpG(A)-STAT3 siRNA conjugates capable of inducing TLR9-dependent gene silencing and activation of primary immune cells such as myeloid dendritic cells, plasmacytoid dendritic cells, and B cells in vitro. TLR9 is also expressed by several human hematologic malignancies, including B-cell lymphoma, multiple myeloma, and acute myeloid leukemia. We further demonstrate that oncogenic proteins such as STAT3 or BCL-X(L) are effectively knocked down by specific CpG(A)-siRNAs in TLR9(+) hematologic tumor cells in vivo. Targeting survival signaling using CpG(A)-siRNAs inhibits the growth of several xenotransplanted multiple myeloma and acute myeloid leukemia tumors. CpG(A)-STAT3 siRNA is immunostimulatory and nontoxic for normal human leukocytes in vitro. The results of the present study show the potential of using tumoricidal/immunostimulatory CpG-siRNA oligonucleotides as a novel 2-pronged therapeutic strategy for hematologic malignancies.
Graphene geometric diodes for optical rectennas (2014)

Optical rectennas, which are micro-antennas to convert optical-frequency radiation to alternating current combined with ultrahigh-speed diodes to rectify the current, can in principle provide high conversion efficiency solar cells and sensitive detectors. Currently investigated optical rectennas using metal/insulator/metal (MIM) diodes are limited in their RC response time and poor impedance matching between diodes and antennas. A new rectifier, the geometric diode, can overcome these limitations. The thesis work has been to develop geometric diode rectennas, along with improving fabrication processes for MIM diode rectennas. The geometric diode consists of a conducting thin-film, currently graphene, patterned into a geometry that leads to diode behavior. In contrast with MIM diodes that have parallel plate electrodes, the planar structure of the geometric diode provides a low RC time constant, on the order of 10-15 s, which permits operation at optical frequencies. Fabricated geometric diodes exhibit asymmetric DC current-voltage characteristics that match well with Monte Carlo simulations based on the Drude model. The measured diode responsivity at DC and zero drain-source bias is 0.012 A/W. Since changing the gate voltage changes the graphene charge carrier concentration and can switch the majority charge type, the rectification polarity of the diode can be reversed. Furthermore, the optical rectification at 28 THz has been measured from rectennas formed by coupling geometric diodes with graphene and metal bowtie antennas. The performance of the rectenna IR detector is among the best reported uncooled IR detectors. The noise equivalent power (NEP) of the rectenna detector using geometric diode was measured to be 2.3 nW Hz-1/2. Further improvement in the diode and antenna design is expected to increase the detector performance by at least a factor of two. Applications for geometric diodes and graphene bowtie antennas include detection of terahertz and optical waves, ultra-high speed electronics, and optical power conversion.
Characterization of an elastase inhibitor produced by Streptomyces lavendulae SMF11 (2000)

An elastase inhibitor, SMFEI02, was isolated from culture broth of Streptomyces lavendulae SMF11. The inhibitor was purified by ultrafiltration followed by XAD-7 column and Dowex-1 anion-exchange chromatographies, and preparative HPLC. The molecular formula was determined to be C14H16N2O2 (MW 244) by HRFAB-MS analysis. The inhibitor was identified to be a diketopiperazine cyclo(S-Phe-S-Pro) by the optical rotation value and NMR spectral data, and showed inhibitory activities for trypsin, chymotrypsin, cathepsin B, and papain as well as elastase with the K(i) values ranging from 1.78 mM to 2.86 μM. The inhibition showed a competitive mode for elastase, chymotrypsin, and cathepsin B, whereas it showed a noncompetitive mode for trypsin and papain.
Double-crowned valved stents for off-pump mitral valve replacement☆ (2005)

Off-pump implantation of a self-expandable valved stent in the mitral position is technically feasible. Further studies will assess if this procedure is also feasible in humans.
Conserved Surface-Exposed K/R-X-K/R Motifs and Net Positive Charge on Poxvirus Complement Control Proteins Serve as Putative Heparin Binding Sites and Contribute to Inhibition of Molecular Interactions with Human Endothelial Cells: a Novel Mechanism for Evasion of Host Defense (2000)

Vaccinia virus complement control protein (VCP) has been shown to possess the ability to inhibit both classical and alternative complement pathway activation. The newly found ability of this protein to bind to heparin has been shown in previous studies to result in uptake by mast cells, possibly promoting tissue persistence. It has also been shown to reduce chemotactic migration of leukocytes by blocking chemokine binding. In addition, this study shows that VCP-through its ability to bind to glycosaminoglycans (heparin-like molecules) on the surface of human endothelial cells-is able to block antibody binding to surface major histocompatibility complex class I molecules. Since heparin binding is critical for many functions of this protein, we have attempted to characterize the molecular basis for this interaction. Segments of this protein, generated by genetic engineering of the DNA encoding VCP into the Pichia pastoris expression system, were used to localize the regions with heparin binding activity. These regions were then analyzed to more specifically define their properties for binding. It was found that the number of putative binding sites (K/R-X-K/R), the overall positive charge, and the percentage of positively charged amino acids within the protein were responsible for this interaction.
Comparison of glass etching to xurography prototyping of microfluidic channels for DNA melting analysis (2007)

Two microchannel manufacturing methods—xurography of double-sided tape and glass etching (lithography and wet etching)—were compared using DNA melting analysis. A heterozygous mutation (3 base-pair deletion) was distinguished from wild type (normal) DNA in 10 nL (xurography and glass etching) and 1 nL (xurography) volumes. The results of the 10 nL and 1 nL melting curves were compared to results using commercial high-resolution instrumentation with 10 µL volumes. These 1000-fold and 10 000-fold volume reductions reduced the signal-to-noise ratio (SNR) only 29-fold and 40-fold for xurography (10 nL and 1 nL, respectively,) and 39-fold for 10 nL glass etched microchannels, still providing adequate discrimination for mutation detection. The reduced SNR of the glass etched microchannels compared to the tape microchannels was due to the in-house bonding process which gave poor optical quality on the surface of the microchip. Xurography of double-sided tape reduces the cost by 20 fold and is four times faster to manufacture than glass etching. Microchips created using the rapid prototyping technique of xurography are a reasonable prototyping alternative to channels created using traditional glass etching for DNA mutation detection.
Lytic infection ofEscherichia colibiofilms by bacteriophage T4 (1995)

Escherichia coli 3000 XIII formed biofilms on the surface of polyvinylchloride coupons in a modified Robbins device. Bacteriophage T4D+ infected cells in the biofilm and replicated. It is commonly held that bacteriophage cannot infect surface-attached bacteria (biofilms) because such bacteria are protected by an exopolymeric matrix that binds macromolecules and prevents their diffusion into the biofilm. To our knowledge this is the first observation that a bacteriophage can infect and multiply within cells growing as a biofilm.
Inhibitory effects of pyrrolidine dithiocarbamate on endotoxin-induced uveitis in Lewis rats. (2002)

These results suggest that PDTC reduces ocular inflammation in eyes with EIU by downregulating proinflammatory cytokine expression and by inhibiting the NF-kappaB-dependent signaling pathway.
Temporal analysis of general control of amino acid biosynthesis in Saccharomyces cerevisiae: role of positive regulatory genes in initiation and maintenance of mRNA derepression. (1984)

In Saccharomyces cerevisiae, starvation for a single amino acid results in the derepression of enzyme activities in multiple amino acid biosynthetic pathways. Derepression is a consequence of increased transcription of the genes encoding these enzymes. Analysis of the kinetics of mRNA elevation established that derepression occurs within 5 min of a shift of the culture from rich medium to starvation medium. Any starvation condition was sufficient to trigger an initial high mRNA elevation; however, it was the severity of starvation which determined the steady-state mRNA levels that were subsequently established. The products of the positive regulatory genes AAS101, AAS103, and AAS2 were shown to be required in the initiation phase of this response, whereas the AAS102 gene product was required to maintain the new elevated steady-state mRNA levels. The AAS101 and AAS102 genes were cloned. Consistent with their respective roles in initiation and maintenance of derepression. AAS101 mRNA was found to be expressed at high levels in both rich and starvation media, whereas AAS102 mRNA was derepressed only under starvation conditions. The derepression of AAS102 mRNA is dependent on the AAS101 gene product.
Neuropeptide Y Receptor Subtypes, Y1 and Y2 (1990)

Heterogeneity among NPY (and PYY) receptors was first proposed on the basis of studies on sympathetic neuroeffector junctions, where NPY (and PYY) can exert three types of action: 1) a direct (e.g., vasoconstrictor) response; 2) a postjunctional potentiating effect on NE-evoked vasoconstriction; and 3) a prejunctional suppression of stimulated NE release; the two latter phenomena are probably reciprocal, since NE affect NPY mechanisms similarly. It was found that amidated C-terminal NPY (or PYY) fragments, e.g., NPY 13-36, could stimulate selectively prejunctional NPY/PYY receptors, which were termed Y2-receptors. Consequently, the postjunctional receptors which were activated poorly by NPY/PYY fragments, were termed Y1-receptors. Later work has indicated that the Y2-receptor may occur postjunctionally in selected sympathetic effector systems. The central nervous system appears to contain a mixture of Y1- and Y2-receptors as indicated by functional as well as binding studies. For instance, NPY and NPY 13-36 produced diametrically opposite effects on behavioral activity, indicating the action of the parent peptide on two distinct receptors. Cell lines, most importantly neuroblastomas, with exclusive populations of Y1- or Y2-receptors, have been characterized by binding and second messenger studies. In this work, selective agonists for the two receptor subtypes were used. Work of many investigators has formed the basis for subclassifying NPY/PYY effects being mediated by either Y1- or Y2-receptors. A preliminary subclassification based on effects of NPY, PYY, fragments and/or analogs is provided in Table 6. It is, however, to be expected that further receptor heterogeneity will be revealed in the future. It is argued that mast cells possess atypical NPY/PYY receptors. The histamine release associated with stimulation of the latter receptors may, at least in part, underlie the capacity of NPY as well as of short C-terminal fragments to reduce blood pressure. Fragments, such as NPY 22-36, appear to be relatively selective vasodepressor agents because of their weak vasopressor properties.(ABSTRACT TRUNCATED AT 400 WORDS)