gebhart/patrepeval huggingface dataset:
Gastric Cytoprotection Is Secondary to Increased Mucosal Fluid Secretion: A Study of Six Cytoprotective Agents in the Rat (1998)

We tested the hypothesis that rapidly developing gastric cytoprotection produced by topical application of exogenous compounds is a result of increased gastric mucosal fluid secretion. Ex vivo gastric chambers were prepared in rats which were subsequently exposed topically to one of the prostaglandin (PG) E1 analogues misoprostol or rioprostil, PGE2, nicotine, N-ethylmaleimide (NEM), 0.25 M HCl, or to their respective vehicles. All agents were added to empty chambers to avoid complications resulting from dilution by gastric contents. Effects of these agents on intraluminal volume changes, blood flow, juxtamucosal pH, histology, and on the mucosal damage resulting from necrotizing agents were studied. All six agents were cytoprotective and each increased net secretion of fluid by the chambered mucosae. Gastric blood flow was not significantly increased by NEM, by 0.25 M HCl, or by nicotine compared to controls, and the juxtamucosal pH was not significantly increased by any of the three agents for which this was studied. Vacuole formation in surface epithelial cells and subepithelial edema were seen after exposure to some agents, but none of the agents led to formation of a thick barrier of exfoliated cells and mucus. Ablation of primary afferent nerves with capsaicin abolished both protection by 0.25 M HCl and the net increase in fluid secretion by the mucosae. Capsaicin ablation did not alter either the protection afforded by NEM or the increase in volume of secretion. We conclude that increased mucosal fluid secretion is the common factor present with all six cytoprotective agents and hence may be the predominant mechanism of cytoprotection against topically applied necrotizing agents.
Antineoplastic Agents 500. Narcistatin,1 (2002)

An efficient procedure was found for synthetic conversion of the sparingly soluble anticancer isocarbostyril narciclasine (1), a component of various Narcissus species, to a cyclic phosphate designated narcistatin (3b). The reaction between narciclasine, tetrabutylammonium dihydrogen phosphate, and p-toluenesulfonic acid in pyridine afforded pyridinium narcistatin (3a) in reasonable yields. Transformation of narcistatin (3a) to, for example, the water-soluble prodrug sodium narcistatin (3d) was easily achieved by cation exchange chromatography. Narcistatin (3b) and 15 salt derivatives were evaluated against a panel of human cancer cell lines, and the range (0.1-0.01) of GI(50) values in micro g/mL was found to parallel that shown by the parent narciclasine.
Liquid-Infused Silicone As a Biofouling-Free Medical Material (2014)

There is a dire need for infection prevention strategies that do not require the use of antibiotics, which exacerbate the rise of multi- and pan-drug resistant infectious organisms. An important target in this area is the bacterial attachment and subsequent biofilm formation on medical devices (e.g., catheters). Here we describe nonfouling, lubricant-infused slippery polymers as proof-of-concept medical materials that are based on oil-infused polydimethylsiloxane (iPDMS). Planar and tubular geometry silicone substrates can be infused with nontoxic silicone oil to create a stable, extremely slippery interface that exhibits exceptionally low bacterial adhesion and prevents biofilm formation. Analysis of a flow culture of <i>Pseudomonas aeruginosa</i> through untreated PDMS and iPDMS tubing shows at least an order of magnitude reduction of biofilm formation on iPDMS, and almost complete absence of biofilm on iPDMS after a gentle water rinse. The iPDMS materials can be applied as a coating on other polymers or prepared by simply immersing silicone tubing in silicone oil, and are compatible with traditional sterilization methods. As a demonstration, we show the preparation of silicone-coated polyurethane catheters and significant reduction of <i>Escherichia coli</i> and <i>Staphylococcus epidermidis</i> biofilm formation on the catheter surface. This work represents an important first step toward a simple and effective means of preventing bacterial adhesion on a wide range of materials used for medical devices.
Magnetic resonance imaging of blood vessels at high fields: In vivo and in vitro measurements and image simulation (1990)

Abstract Unusually high image contrast in vivo magnetic resonance imaging of the brain becomes observable at high magnetic fields when the blood oxygenation level is lowered. The cause of the contrast has been attributed to a magnetic susceptibility effect induced by paramagnetic deoxyhemoglobin in red cells. When the cylinder axis of a blood vessel is not parallel to the main magnetic field, the susceptibility difference produces varying local fields around the blood vessel. In gradient‐echo images, not in spin‐echo images, these local fields cause intravoxel dephasing of the water signal of the surrounding tissue. This description of the contrast enhancement has been confirmed by a series of in vitro blood sample experiments and image simulations. A predicted contrast change has been demonstrated in brain images of a mouse placed at two different orientations in the magnet. From the simulated images, the dependence of the contrast on the field strength has been estimated. © 1990 Academic Press, Inc.
Blockade of Programmed Death-1 Ligands on Dendritic Cells Enhances T Cell Activation and Cytokine Production (2003)

Programmed death-1 ligand (PD-L)1 and PD-L2 are ligands for programmed death-1 (PD-1), a member of the CD28/CTLA4 family expressed on activated lymphoid cells. PD-1 contains an immunoreceptor tyrosine-based inhibitory motif and mice deficient in PD-1 develop autoimmune disorders suggesting a defect in peripheral tolerance. Human PD-L1 and PD-L2 are expressed on immature dendritic cells (iDC) and mature dendritic cells (mDC), IFN-gamma-treated monocytes, and follicular dendritic cells. Using mAbs, we show that blockade of PD-L2 on dendritic cells results in enhanced T cell proliferation and cytokine production, including that of IFN-gamma and IL-10, while blockade of PD-L1 results in similar, more modest, effects. Blockade of both PD-L1 and PD-L2 showed an additive effect. Both whole mAb and Fab enhanced T cell activation, showing that PD-L1 and PD-L2 function to inhibit T cell activation. Enhancement of T cell activation was most pronounced with weak APC, such as iDCs and IL-10-pretreated mDCs, and less pronounced with strong APC such as mDCs. These data are consistent with the hypothesis that iDC have a balance of stimulatory vs inhibitory molecules that favors inhibition, and indicate that PD-L1 and PD-L2 contribute to the poor stimulatory capacity of iDC. PD-L1 expression differs from PD-L2 in that PD-L1 is expressed on activated T cells, placental trophoblasts, myocardial endothelium, and cortical thymic epithelial cells. In contrast, PD-L2 is expressed on placental endothelium and medullary thymic epithelial cells. PD-L1 is also highly expressed on most carcinomas but minimally expressed on adjacent normal tissue suggesting a role in attenuating antitumor immune responses.
AggR, a transcriptional activator of aggregative adherence fimbria I expression in enteroaggregative Escherichia coli (1994)

Enteroaggregative Escherichia coli (EAggEC) has been associated with persistent pediatric diarrhea in the developing world, yet the pathogenetic mechanisms of EAggEC infection are unknown. Our previous data have suggested that aggregative adherence of some EAggEC strains to HEp-2 cells is mediated by flexible, bundle-forming fimbriae, which we have termed aggregative adherence fimbriae I (AAF/I). Genes sufficient to confer expression of AAF/I are located on the 60-MDa plasmid of EAggEC 17-2; AAF/I genes are present as two unlinked plasmid regions (regions 1 and 2), separated by 9 kb of DNA. Here we report the complete DNA sequencing of region 2 and the identification of an open reading frame which is involved in the expression of AAF/I. One open reading frame of 794 bp encodes a protein (designated AggR) with a predicted molecular size of 29.4 kDa, which shows a high degree of amino acid sequence identity to CfaR and other members of the AraC class of gene regulators. The cloned aggR gene (or, alternatively, a cloned cfaR gene) was sufficient to complement a region 1 clone to confer AAF/I expression. To further substantiate the role of aggR in the regulation of AAF/I, we constructed a 289-bp in-frame aggR deletion and replaced the native gene in 17-2 by allelic exchange, using the temperature-sensitive vector pIB307. The resulting aggR deletions were negative for AAF/I expression, but expression was restored when the aggR gene (cloned into pBluescript II SK) was reintroduced into the aggR mutant. RNA slot blot experiments using a probe for the putative AAF/I pilin subunit (aggA) revealed that aggR operates as a transcriptional activator of aggA expression. aggA::phoA fusions were constructed in 17-2 and in 17-2 delta aggR. AggR was found to promote expression of the aggA gene under a variety of conditions of temperature, osmolarity, oxygen tension, and medium. At acid pH, aggA expression was maximal and was regulated by both AggR-dependent and AggR-independent mechanisms.
An analytic model of hierarchical mass storage systems with network-attached storage devices (1996)

Network attached storage devices improve I/O performance by separating control and data paths and eliminating host intervention during data transfer. Devices are attached to a high speed network for data transfer and to a slower network for control messages. Hierarchical mass storage systems use disks to cache the most recently used files and tapes (robotic and manually mounted) to store the bulk of the files in the file system. This paper shows how queuing network models can be used to assess the performance of hierarchical mass storage systems that use network attached storage devices. The analytic model validated through simulation was used to analyze many different scenarios.
Xotch , the Xenopus Homolog of Drosophila Notch (1990)

During the development of a vertebrate embryo, cell fate is determined by inductive signals passing between neighboring tissues. Such determinative interactions have been difficult to characterize fully without knowledge of the molecular mechanisms involved. Mutations of Drosophila and the nematode Caenorhabditis elegans have been isolated that define a family of related gene products involved in similar types of cellular inductions. One of these genes, the Notch gene from Drosophila, is involved with cell fate choices in the neurogenic region of the blastoderm, in the developing nervous system, and in the eye-antennal imaginal disc. Complementary DNA clones were isolated from Xenopus embryos with Notch DNA in order to investigate whether cell-cell interactions in vertebrate embryos also depend on Notch-like molecules. This approach identified a Xenopus molecule, Xotch, which is remarkably similar to Drosophila Notch in both structure and developmental expression.
Targeting of High-Capacity Adenoviral Vectors (2001)

High-capacity adenoviral (HC-Ad) vectors contain only the noncoding termini of the viral genome, can deliver large DNA fragments of up to 36 kb into target cells, and feature reduced toxicity and prolonged transgene expression in vivo. To enhance the potential of HC-Ad vectors to transduce specific cell types, we constructed a versatile infectious new helper virus plasmid that can be used readily to introduce peptide ligands into the HI loop of the fiber knob domain of Ad5-based HC-Ad vectors. Helper viruses with a 6x-His epitope or Arg-Gly-Asp (RGD) peptide insertion retained the full infectivity of the wild-type helper virus. The RGD-modified helper virus was used for production of a capsid-modified HC-Ad vector expressing beta-galactosidase. The RGD HC-Ad vector transduced the ovarian carcinoma cell lines SK-OV-3 and OVCAR-3 with 4- to 20-fold higher efficiency, compared to unmodified vectors. Transduction of both primary vascular smooth muscle cells as well as primary human endothelial cells was increased up to 15-fold with the RGD-modified vector. Competition experiments with recombinant knob protein and different RGD peptides indicated that the RGD-mediated transduction was Coxsackie and Adenovirus receptor (CAR)-independent and involved integrin alpha(v)beta(5). The use of fiber-modified helper viruses in the last amplification step of HC-Ad vector production allows for convenient and efficient targeting of these vectors towards different cell types. Targeting strategies will increase the spectrum of applications for HC-Ad vectors and will further add to their safety.
A Non-antibacterial Chemically-modified Tetracycline Inhibits Mammalian Collagenase Activity (1987)

Tetracyclines (including the semi-synthetic analogues, minocycline and doxycycline) are considered useful adjuncts in periodontal therapy because they suppress Gram-negative periodontopathogens. Recently, these antibiotics were found to inhibit mammalian collagenase activity, a property which may also be of therapeutic value. It has been suggested that the anti-collagenase properties of the tetracyclines are independent of their antibiotic efficacy. To advance this hypothesis further, we chemically converted tetracycline hydrochloride to its non-antimicrobial analogue, de-dimethylaminotetracycline. This chemically-modified tetracycline (CMT), although no longer an effective antibiotic, was found to inhibit the in vitro activity of collagenase from partially purified extracts of human rheumatoid synovial tissue and rachitic rat epiphysis. In a preliminary in vivo study, pathologically-excessive collagenase in skin and gingiva was induced by rendering adult male rats diabetic, and the oral administration of CMT to these rats significantly reduced the excessive collagenase activity in both tissues. Moreover, CMT administration did not affect the severe hyperglycemia in these rats but did prevent, at least in part, the diabetes-induced loss of body weight, skin weight, and skin collagen mass; these effects suggest a lack of toxicity in this animal model. A proposed clinical advantage of CMT over conventional tetracyclines, in the treatment of diseases characterized by excessive collagenolytic activity, is the lack of development of antibiotic-resistant micro-organisms during prolonged use. However, the consideration of clinical trials to support this hypothesis must await further laboratory and extensive toxicity tests.
Counter-based cache replacement algorithms (2006)

Recent studies have shown that in highly associative caches, the performance gap between the least recently used (LRU) and the theoretical optimal replacement algorithms is large, suggesting that alternative replacement algorithms can improve the performance of the cache. One main reason for this performance gap is that in the LRU replacement algorithm, a line is only evicted after it becomes the LRU line, long after its last access/touch, while unnecessarily occupying the cache space for a long time. This paper proposes a new approach to deal with the problem: counter-based L2 cache replacement. In this approach, each line in the L2 cache is augmented with an event counter that is incremented when an event of interest, such as a cache access to the same set, occurs. When the counter exceeds a threshold, the line "expires", and becomes evictable. When expired lines are evicted early from the cache, they make extra space for lines that may be more useful, reducing the number of capacity and conflict misses. Each line's threshold is unique and is dynamically learned and stored in a small 40-Kbyte counter prediction table. We propose two new replacement algorithms: access interval predictor (AIP) and live-time predictor (LvP). AIP and LvP speed up 10 (out of 21) SPEC2000 benchmarks by up to 40% and 11% on average.
Crystal Structures of Novel Allosteric Peptide Inhibitors of HIV Integrase Identify New Interactions at the LEDGF Binding Site (2011)

An optimised method of solution cyclisation gave us access to a series of peptides including SLKIDNLD (2). We investigated the crystallographic complexes of the HIV integrase (HIV-IN) catalytic core domain with 13 of the peptides and identified multiple interactions at the binding site, including hydrogen bonds with residues Thr125 and Gln95, that have not previously been described as being accessible within the binding site. We show that the peptides inhibit the interaction of lens epithelium-derived growth factor (LEDGF) with HIV-IN in a proximity AlphaScreen assay and in an assay for the LEDGF enhancement of HIV-IN strand transfer. The interactions identified represent a potential framework for the development of new HIV-IN inhibitors.
ConvAI at SemEval-2019 Task 6: Offensive Language Identification and Categorization with Perspective and BERT (2019)

This paper presents the application of two strong baseline systems for toxicity detection and evaluates their performance in identifying and categorizing offensive language in social media. Perspective is an API, that serves multiple machine learning models for the improvement of conversations online, as well as a toxicity detection system, trained on a wide variety of comments from platforms across the Internet. BERT is a recently popular language representation model, fine tuned per task and achieving state of the art performance in multiple NLP tasks. Perspective performed better than BERT in detecting toxicity, but BERT was much better in categorizing the offensive type. Both baselines were ranked surprisingly high in the SEMEVAL-2019 OFFENSE-VAL competition, Perspective in detecting an offensive post (12th) and BERT in categorizing it (11th). The main contribution of this paper is the assessment of two strong baselines for the identification (Perspective) and the categorization (BERT) of offensive language with little or no additional training data.
TMS stimulator design (2012)

Transcranial magnetic stimulators have progressed from basic implementations to integrated systems optimized for treatment of pathologies. This article reviews key factors of design of such clinically targeted systems, discussing design principles, procedure-specific features, and clinical safety requirements. A power source, a capacitor, and a high-power switch controlled by a processor form the basic stimulator. The fundamental operating mechanism of a TMS stimulator is to create a changing magnetic field that can induce a current in adjacent conductive material. The clinical TMS system must incorporate patient positioning, patient comfort, coil positioning features, and intuitive user controls and means of managing patient data to be a fully effective system. The most important safety risk with repetitive TMS reported in the literature is the risk of inducing seizure. Other safety considerations include proper use of human factor analysis to minimize improper operation, the biocompatibility of materials touching the patient, and addressing acoustic noise.
SELF-SIMILARITY AND THE GEOMETRIC REQUIREMENTS FOR FREQUENCY INDEPENDENCE IN ANTENNAE (1999)

Self-similarity and origin symmetry are shown to be the key geometric constraints in the determination of frequency independent properties of antennae. Fractal antennae with origin symmetry meet these criteria of the extended version of Rumsey's principle. Frequency independence is not achieved by self-similarity alone. Self-complementarity plays no role in frequency independence, but does aid in smoothing out impedance variations for coarsely iterated frequency independent antennae. New families of practical designs arise from these geometric insights, which need not follow the usual constraints of angle-defined structure of the original Rumsey's principle.
Three-dimensional imaging of objects embedded in turbid media with fluorescence and Raman spectroscopy (1995)

We present a single-ended technique for three-dimensional imaging of objects embedded in a turbid medium by the use of time-resolved fluorescence emission or Raman scattering. The technique uses the earliest arriving photons, which we show are not sensitive to the relatively long fluorescence lifetime, and thus can be used to extract the desired spatial information accurately, even at a distance equivalent to 100 mean free paths. The results also demonstrate the feasibility and the potential of one's combining time-resolved optical tomography with fluorescence or Raman spectroscopy to localize and identify the embedded objects. This technique may be valuable for the diagnosis of disease in highly scattering human tissue because it can provide spatial and biochemical information about the composition of embedded lesions.
Identification of a putative thromboxane A2/prostaglandin H2 receptor in human platelet membranes. (1986)

The binding of the competitive thromboxane A2/prostaglandin H2 (TXA2/PGH2) antagonist (9,11-dimethylmethano-11, 12-methano-16-(3-aza-15 alpha beta-omega-tetranor-TXA2) ([125I]PTA-OH) to membranes prepared from human platelets was characterized. [125I]PTA-OH binding to membranes from human platelets was saturable, displaceable, and dependent on protein concentration. Scatchard analysis of equilibrium binding carried out at 30 degrees C revealed one class of binding sites with a Kd of 30 +/- 4 nM and a Bmax of 1.8 +/- 0.3 pmol/mg of protein (n = 5). Kinetic analysis of the binding of [125I]PTA-OH at 0 degrees C yielded a k1 of 1.35 X 10(6) M-1 min-1 and a k-1 of 0.032 min-1, Kd = k-1/k1 = 24 nM. The potencies of a series of TXA2/PGH2 antagonists as inhibitors of [125I]PTA-OH binding was correlated with their potencies as inhibitors of platelet aggregation induced by the TXA2/PGH2 mimetic, U46619 (1 microM) (r = 0.93, p less than 0.01). A series of TXA2/PGH2 mimetics also displaced [125I]PTA-OH from its binding site, and their potencies as inhibitors of [125I]PTA-OH binding were correlated with their potencies as stimulators of platelet aggregation (r = 0.91, p less than 0.05). The IC50 values for displacement of [125I]PTA-OH by PGF2 alpha, PGD2, and the stable PGI2 analog Iloprost were greater than 25 microM, suggesting that [125I]PTA-OH does not bind to other known platelet prostaglandin receptors. These data are consistent with the notion that this binding site may represent the platelet TXA2/PGH2 receptor.
Development of Bovine Nuclear Transfer Embryos Made with Oogonia1 (1997)

The pluripotency of embryonic germ cells in the mouse suggests that mitotic bovine fetal germ cells might also be a source of pluripotent cells. To investigate the pluripotency of bovine oogonia, the development in vitro of bovine embryos reconstructed by fusing oogonia with enucleated oocytes was compared with that of embryos made similarly with either blastomeres or granulosa cells. The donor cells (fresh oogonia, cryopreserved oogonia, 16- to 32-cell-stage blastomeres, or granulosa cells) were fused to the enucleated oocytes electrically. The proportions of reconstructed embryos that had cleaved at 40 h after fusion using these types of donor cells were not significantly different (37%, 33%, 56%, and 31%, respectively; p > 0.05). However, the proportions of cleaved reconstructed embryos that developed to the blastocyst stage were 9%, 13%, 36%, and 3%, respectively, significantly higher (p < or = 0.05) with blastomeres than with the other three types of donor cells. After transfer of 3 morulae and 4 blastocysts made with oogonia into three recipient heifers, embryonic and extra-embryonic tissues developed in one animal. On recovery after 43 days gestation, this conceptus was shown to be genetically identical, at 11 microsatellite loci, to the fetus that had provided the oogonia. Cytological analysis of the embryos made with oogonia at 40-44 h after fusion and at the morula and blastocyst stages revealed that aberrant cytokinesis and nucleokinesis had given rise to multinucleated, anucleate, and polyploid cells in the reconstructed embryos. It is concluded that limited pluripotency of bovine oogonia has been demonstrated, warranting further study in this area.