gebhart/patrepeval huggingface dataset:
Effects of Perioperative Dexmedetomidine Infusion in Patients Undergoing Vascular Surgery (1995)

Infusion of dexmedetomidine up to a targeted plasma concentration of 0.45 ng/ml appears to benefit perioperative hemodynamic management of surgical patients undergoing vascular surgery but required greater intraoperative pharmacologic intervention to support blood pressure and heart rate.
Nivolumab effectively inhibit platinum-resistant ovarian cancer cells via induction of cell apoptosis and inhibition of ADAM17 expression. (2017)

Therefore, all the results demonstrated that the combined treatment with nivolumab and cisplatin effectively inhibited PROC cells via induction of cell apoptosis and inhibition of ADAM17 expression.
Obstructive Nephropathy in the Mouse (2001)

The infiltration of leukocytes plays a major role in mediating tubulointerstitial inflammation and fibrosis in chronic renal disease. CC chemokines participate in leukocyte migration and infiltration into inflamed renal tissue. Because CC chemokine-directed leukocyte migration is mediated by target cell expression of a group of CC chemokine receptors, this study examined the expression of CC chemokines and their receptors during initiation of tubulointerstitial fibrosis after unilateral ureteral obstruction in C57BL/6 mice. Obstructed kidneys developed hydronephrosis, tubular cell damage, interstitial inflammation, and fibrosis. From days 2 to 10, a progressive interstitial influx of F4/80+ macrophages and CD3+ lymphocytes occurred (macrophages, 4-fold; lymphocytes, 20-fold at day 10, compared with contralateral control kidneys). In parallel, the number of activated fibroblast-specific protein 1+ fibroblasts and interstitial collagen IV accumulation increased from days 2 to 10. The mRNA expression of CC chemokines (predominantly monocyte chemoattractant protein-1 [MCP-1]/CCL2, RANTES/CCL5) and their receptors CCR1, CCR2, CCR5 increased progressively from days 2 to 10. By in situ hybridization, a prominent interstitial mRNA expression of MCP-1 and RANTES and their receptors CCR2 and CCR5 localized to interstitial mononuclear cell infiltrates. MCP-1 and RANTES expression was also seen in tubular epithelial cells. Fluorescence-activated cell sorter analysis of single-cell suspensions from obstructed kidneys revealed a prominent expression of CCR2 and CCR5 by infiltrating macrophages, whereas most lymphocytes expressed CCR5 only. These data demonstrate an increased expression of MCP-1/CCL2 and RANTES/CCL5 at sites of tubulointerstitial damage and progressive fibrosis during unilateral ureteral obstruction that correlates with simultaneous accumulation of interstitial macrophages and T lymphocytes expressing the respective surface receptors CCR2 and CCR5. The chemokine receptor-mediated leukocyte influx into the tubulointerstitium could offer a new potential target for therapeutic intervention in progressive renal tubulointerstitial fibrosis.
Large area fine line patterning by scanning projection lithography (1995)

A new type of photolithography tool has been developed, addressing the specific needs of MCM manufacture. It is based on scanning projection exposure. It can expose panels at variable sizes up to 500 mm by 600 mm (typical laminate size), with an optical resolution of less than 5 /spl mu/m and an overlay accuracy of 2 /spl mu/m (typical thin film design rules). With the exposure being a mask projection, mask damage and subsequent yield problems are generally avoided.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Electrophilic fluorination of arylatrialkultin derivatives with caesium fluoroxysulphate (1986)

M. R. Bryce, R. D. Chambers, S. T. Mullins and A. Parkin, J. Chem. Soc., Chem. Commun., 1986, 1623 DOI: 10.1039/C39860001623
Core Formation in Escherichia coli Bacterioferritin Requires a Functional Ferroxidase Center (2003)

Bacterioferritin from Escherichia coli is able to accumulate large quantities of iron in the form of an inorganic iron(III) mineral core. Core formation in the wild-type protein and a number of ferroxidase center variants was studied to determine key features of the core formation process and, in particular, the role played by the ferroxidase center. Core formation rates were found to be iron(II)-dependent and also depended on the amount of iron already present in the core, indicating the importance of the core surface in the mineralization reaction. Core formation was also found to be pH-dependent in terms of both rate and iron-loading characteristics, occurring with maximum efficiency at pH 6.5. Even at this optimum pH, however, the effective iron capacity was approximately 2700 per molecule, i.e., well below the theoretical limit of approximately 4500, suggesting that competing oxidation/precipitation processes have a major influence on the amount of iron accumulated. Disruption of the ferroxidase center, by site-directed mutagenesis or by chemical inhibition with zinc(II), had a profound effect on core formation. Effective iron capacities were found to be linked to iron(II) oxidation rates, and in zinc(II)-inhibited wild-type and E18A bacterioferritins core formation was severely restricted. Zinc(II) was also able, even at low stoichiometries (12-60 ions/protein), to significantly inhibit further core formation in protein already containing a substantial core, indicating the importance of the ferroxidase center throughout the core formation process. A mechanism is proposed that incorporates essential roles for the core surface and the ferroxidase center. A central feature of this mechanism is that dioxygen cannot readily gain access to the core, perhaps because the channels through the bacterioferritin coat are hydrophilic and dioxygen is nonpolar.
Gap junctions play a role in the 'bystander effect' of the herpes simplex virus thymidine kinase/ganciclovir system in vitro. (1996)

Tumor cells transduced with the herpes simplex virus thymidine kinase (HSVtk) gene are sensitive to the anti-viral drug ganciclovir (GCV). However, nearby untransduced tumor cells are also efficiently killed. The mechanism of this 'bystander effect' was studied by comparing pairs of tumor cell lines transfected with connexin genes that differed only in their degree of gap junctional communication. More efficient cell killing was uniformly seen in connexin transfectants compared with the less coupled cell lines. These results provide direct evidence that gap junctional communication plays an important role in mediating the bystander effect of the HSVtk/GCV system in vitro and have important prognostic and therapeutic implications for future gene therapy trials.
Structural and Functional Analyses of the Human Toll-like Receptor 3 (2006)

Toll-like receptors (TLRs) play critical roles in bridging the innate and adaptive immune responses. The human TLR3 recognizes foreign-derived double-stranded RNA and endogenous necrotic cell RNA as ligands. Herein we characterized the contribution of glycosylation to TLR3 structure and function. Exogenous addition of purified extracellular domain of TLR3 (hTLR3 ECD) expressed in human embryonic kidney cells was found to inhibit TLR3-dependent signaling, thus providing a reagent for structural and functional characterization. Approximately 35% of the mass of the hTLR3 ECD was due to posttranslational modification, with N-linked glycosyl groups contributing substantially to the additional mass. Cells treated with tunicamycin, an inhibitor of glycosylation, prevented TLR3-induced NF-kappaB activation, confirming that N-linked glycosylation is required for bioactivity of this receptor. Further, mutations in two of these predicted glycosylation sites impaired TLR3 signaling without obviously affecting the expression of the protein. Single-particle structures reconstructed from electron microscopy images and two-dimensional crystallization revealed that hTLR3 ECD forms a horseshoe structure similar to the recently elucidated x-ray structure of the protein expressed in insect cells using baculovirus vectors (Choe, J., Kelker, M. S., and Wilson, I. A. (2005) Science 309, 581-585 and Bell, J. K., Botos, I., Hall, P. R., Askins, J., Shiloach, J., Segal, D. M., and Davies, D. R. (2005) Proc. Natl. Acad. Sci. U. S. A. 102, 10976-10980). There are, however, notable differences between the human cell-derived and insect cell-derived structures, including features attributable to glycosylation.
Crystallization and preliminary X-ray diffraction analysis of recombinant hepatitis E virus-like particle (2008)

Hepatitis E virus (HEV) accounts for the majority of enterically transmitted hepatitis infections worldwide. Currently, there is no specific treatment for or vaccine against HEV. The major structural protein is derived from open reading frame (ORF) 2 of the viral genome. A potential oral vaccine is provided by the virus-like particles formed by a protein construct of partial ORF3 protein (residue 70-123) fused to the N-terminus of the ORF2 protein (residues 112-608). Single crystals obtained by the hanging-drop vapour-diffusion method at 293 K diffract X-rays to 8.3 A resolution. The crystals belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 337, b = 343, c = 346 A, alpha = beta = gamma = 90 degrees , and contain one particle per asymmetric unit.
A Theoretical Framework to Represent Narrative Structures for Visual Storytelling (2015)

In this paper, we present a theoretical framework to represent and manipulate narrative structures for visual storytelling. This framework can be used in applications beyond visual storytelling, which includes formal representation of stories, emotional, social and even economical interactions among agents. Our framework significantly extends and formalizes classical narratology theories. In our framework, we represent narratological functions as interventions by employing an extension of causal inference theory, as directed graphs that provide cause and effect relationships among agents. Moreover, we categorize them as real, expressed and observed interventions. This differentiation allows us to represent beliefs, lies and misunderstandings. In our framework, any transformation in causality graph structure is called an event by providing a non-linear temporal dimension that can even allow timetravel. This approach provides a general framework to develop tools for modeling narration and can help to investigate social and economic interactions.
Efficacy of Dendritic Cells Matured Early with OK-432 (Picibanil®), Prostaglandin E2, and Interferon-α as a Vaccine for a Hormone Refractory Prostate Cancer Cell Line (2010)

Dendritic cells (DCs) are potent antigen-presenting cells. OK432 (Picibanil) was introduced as a potent stimulator of DC maturation in combination with prostaglandin-E(2) and interferon-alpha. We compared the efficacy of a DC-prostate cancer vaccine using early-mature DCs stimulated with OK432, PGE2 and INF-alpha (OPA) with that of vaccines using other methods. On days 3 or 7 of DC culture, TNF-alpha (T), TNF-alpha and LPS (TL) or OPA were employed as maturation stimulators. DU145 cells subjected to heat stress were hybridized with mature DCs using polyethyleneglycol. T cells were sensitized by the hybrids, and their proliferative and cytokine secretion activities and cytotoxicity were measured. The yields of early-mature DCs were higher, compared to yields at the conventional maturation time (P<0.05). In the early maturation setting, the mean fusion ratios, calculated from the fraction of dual-positive cells, were 13.3%, 18.6%, and 39.9%, respectively (P=0.051) in the T only, TL, and OPA-treated groups. The function of cytotoxic T cells, which were sensitized with the hybrids containing DCs matured early with OPA, was superior to that using other methods. The antitumor effects of DC-DU145 hybrids generated with DCs subjected to early maturation with the OPA may be superior to that of the hybrids using conventional maturation methods.
Mosquito cells infected with vesicular stomatitis virus yield unsialylated virions of low infectivity (1975)

Vesicular stomatitis virus propagated in and released from Aedes albopictus cells had the normal complement of viral proteins; the glycoprotein contained carbohydrate but no sialic acid. These virions had markedly reduced hemagglutinating activity and exhibited a very high ratio of physical particles to infectious virus. In vitro sialylation of vesicular stomatitis virions grown in mosquito cells resulted in a 100-fold increase in both infectivity and hemagglutination titers to levels approaching those of virus grown in BHK-21 cells. These experiments provide an example of host-controlled modification of viral infectivity.
Molecular cloning and charcterization of rat estrogen receptor cDNA (1987)

A cDNA clone of rat uterus estrogen receptor (ER) has been isolated and sequenced. This clone contains a complete open reading frame encoding 600 amino acid residues which is 5 and 11 amino acids larger than the corresponding molecules of human and chicken, respectively. The molecular weight of this protein is calculated to be 67,029. When this clone was ligated to the pSV2 vector and transfected into COS7 cells, a protein was produced that had the same affinity to estrogen as rat uterus ER. This sequence shows 88% homology with human ER; 528 amino acids are identical and 14 amino acids are conservative substitutions. The comparison of rat, human and chicken ER sequences indicate the presence of three highly conserved regions suggesting that these regions play important roles in ER function. The putative DNA-binding domain is completely identical in rat, human and chicken. The C-terminal half region which is thought to be the estrogen binding domain is also highly conserved and is rich in hydrophobic amino acid residues. Southern blot analysis of genomic DNA with ER cDNA aa a probe has shown that related sequences are present in the genome.
Radioisotope concentrator gene therapy using the sodium/iodide symporter gene. (1999)

We demonstrate a novel method of concentrating radiation for tumor imaging or killing. The rat sodium/iodide symporter gene (rNIS) was cloned into a retroviral vector for transfer into cancer cells to mimic the iodide uptake of thyroid follicular cells. In vitro iodide transport shows that the symporter functions similarly in rNIS-transduced tumor cells and rat thyroid follicular cells. rNIS-transduced and control nontransduced (NV) human A375 melanoma xenografts established in vivo in athymic nude mice were imaged using a gamma camera after i.p. injections of 123I. The rNIS-transduced human A375 melanoma tumors are visually distinguishable from and accumulate significantly more radionuclides than NV tumors. In vitro clonogenic assays confirm efficacy and clearly show that rNIS-transduced A375 human melanoma, BNL.1 ME murine transformed liver, CT26 murine colon carcinoma, and IGROV human ovarian carcinoma can be selectively killed by the induced accumulation of 131I. Thus, NIS-based gene therapy may have both diagnostic and therapeutic applications for cancer.
Synthesis and activity of NH2‐ and COOH‐terminal elastase recognition sequences on cotton (1999)

The application of peptide recognition sequences of elastase to fibers of wound dressings is a possible route to inhibiting high levels of destructive elastase in the chronic wound. For this reason we have synthesized the elastase recognition sequence Val-Pro-Val on both cotton cellulose, and carboxymethylated cellulose cotton (CMC) and prepared chromatography columns of these to examine elastase retention. The tripeptide was synthesized on cotton-based cellulose fibers both in sequence and as a tripeptide methyl ester. Glycine was employed as a linker of the recognition sequence to the cotton cellulose. Pre-treatment of cotton cellulose with cellulase improved the substitution level of glycine. The peptidocellulose conjugates were employed as a chromatographic stationary phase to assess elastase retention. The sequence Val-Pro-Val-OMe was amino-terminally anchored to carboxymethylated cotton and demonstrated retention of up to 58% of elastase when first applied to the column. Higher repetitive retention was demonstrated subsequently. Cotton gauze similarly modified with Val-Pro-Val-Gly cellulose was compared with untreated gauze for reduction of elastase activity in buffered saline. Solutions of elastase that were treated with Val-Pro-Val-Gly cellulose cotton gauze, demonstrated reduced elastase activity. This study demonstrates the use of elastase recognition sequences as sequestering agents of elastase when attached to cotton fibers and constitutes a model for the design of peptidocellulose analogs in dressing fibers for chronic wounds.
Evolution of an organophosphate-degrading enzyme: a comparison of natural and directed evolution (2003)

Organophosphate-degrading enzyme from Agrobacterium radiobacter P230 (OPDA) is a recently discovered enzyme that degrades a broad range of organophosphates. It is very similar to OPH first isolated from Pseudomonas diminuta MG. Despite a high level of sequence identity, OPH and OPDA exhibit different substrate specificities. We report here the structure of OPDA and identify regions of the protein that are likely to give it a preference for substrates that have shorter alkyl substituents. Directed evolution was used to evolve a series of OPH mutants that had activities similar to those of OPDA. Mutants were selected for on the basis of their ability to degrade a number of substrates. The mutations tended to cluster in particular regions of the protein and in most cases, these regions were where OPH and OPDA had significant differences in their sequences.
Attachment of pneumococcal autolysin to wall teichoic acids, an essential step in enzymatic wall degradation (1984)

High concentrations of choline and phosphorylcholine blocked the adsorption of pneumococcal autolytic enzyme to homologous cell walls and inhibited enzymatic cell wall hydrolysis in a noncompetitive manner. Enzyme adsorption had an absolute requirement for the presence of choline residues in the wall teichoic acid. Other amino alcohols and derivatives such as ethanolamine, monomethylaminoethanolamine , and phosphorylethanolamine had no effect on enzyme adsorption or hydrolytic activity. It is proposed that enzymatic hydrolysis of cell walls requires prior adsorption of enzyme molecules to the insoluble wall substrate and that cholin residues of the wall teichoic acid have the role of adsorption ligands in this process.
Electro‐osmotic Drag Coefficient of Water and Methanol in Polymer Electrolytes at Elevated Temperatures (1996)

The electro‐osmotic drag coefficient of water in two polymer electrolytes was experimentally determined as a function of water activity and current density for temperatures up to 200°C. The results show that the electro‐osmotic drag coefficient varies from 0.2 to 0.6 in Nafion®/ membrane electrolyte, but is essentially zero in phosphoric acid‐doped FBI (polybenzimidazole) membrane electrolyte over the range of water activity considered. The near‐zero electro‐osmotic drag coefficient found in PBI indicates that this electrolyte should lessen the problems associated with water redistribution in proton exchange membrane fuel cells.
A Drosophila CREB/CREM Homolog Encodes Multiple Isoforms, Including a Cyclic AMP-Dependent Protein Kinase-Responsive Transcriptional Activator and Antagonist (1995)

We have characterized a Drosophila gene that is a highly conserved homolog of the mammalian cyclic AMP (cAMP)-responsive transcription factors CREB and CREM. Uniquely among Drosophila genes characterized to date, it codes for a cAMP-responsive transcriptional activator. An alternatively spliced product of the same gene is a specific antagonist of cAMP-inducible transcription. Analysis of the splicing pattern of the gene suggests that the gene may be the predecessor of the mammalian CREB and CREM genes.
Correlation of efficacy between EGFR gene copy number and lapatinib/capecitabine therapy in HER2-positive metastatic breast cancer. (2010)

1059 Background: Lapatinib (L) is a selective dual EGFR and HER2 inhibitor. In HER2-positive metastatic breast cancer pretreated with trastuzumab-based therapies, the association of L + capecitabine (C) showed superior response rate (Rr) and progression-free survival (PFS) over C alone. We analyzed the correlation between EGFR gene copy number (GCn) and clinical outcome in a population treated with L 1,250 mg p.o. daily plus C 2,000 mg/m2 p.o. days 1-14 q 21. HER3 status by immunohistochemistry was also evaluated. Methods: EGFR GCn was assessed by FISH analysis in paraffin-embedded tissue blocks from HER2-positive patients who had failed at least one trastuzumab-based therapy in the metastatic setting. EGFR gene status was scored as: the mean value of EGFR GCn per nucleus, the mean ratio between EGFR and chromosome 7, and the percentage of cells displaying > 5 EGFR GCN. A receiver operating characteristic (ROC) analysis was set up to define the cut-off of mean EGFR GCn. A value > 3.36 was able to discriminate responders versus nonresponders. Primary end point of the study was identification of the EGFR FISH score that could best predict Rr. Results: Among 44 patients treated with L+C, 37 were evaluable for EGFR FISH analysis. No sample displayed a homogeneous amplification of the EGFR gene by ratio (EGFR gene/CEP 7 ≥2). Patients characteristics were: median age 53 (range 28-75), visceral disease in 34 patients (85%), median number of previous trastuzumab-based therapies was 2 (1-5). Mean EGFR GCn was > 3.36 in 13/37 patients. These patients showed a significantly higher Rr (n=9/13; 69%) compared to those with mean EGFR GCn ≤ 3.36 (n= 4/13; 30%), (p=0.009). The status of HER3 was not associated with response. No significant differences in terms of both PFS and overall survival according to EGFR GCn were seen (p=0.90 and p=0.52, respectively). Conclusions: High EGFR GCn may predict for increased sensitivity to L + C. HER3 protein overexpression does not seem to correlate with response to L + C. This is the first report associating increased EGFR GCn with response to L. These results warrant further investigation. No significant financial relationships to disclose.
List Viterbi algorithms for continuous transmission (2001)

The conventional list Viterbi algorithm (LVA) produces a list of the L best output sequences over a certain block length in decoding a terminated convolutional code. We show in this paper that the LVA with a sufficiently long list is an optimum maximum-likelihood decoder for the concatenated pair of a convolutional code and a cyclic redundancy check (CRC) block code with error detection. The CRC is used to select the output. New LVAs for continuous transmission are proposed and evaluated, where no termination bits are required for the convolutional code for every CRC block. We also present optimum and suboptimum LVAs for tailbiting convolutional codes. Convolutional codes with Viterbi decoding were proposed for so-called hybrid in band on channel (hybrid IBOC) systems for digital audio broadcasting compatible with the frequency modulation band. For high-quality audio signals, it is beneficial to use error concealment/error mitigation techniques to avoid the worst type of channel errors. This requires a reliable error flag mechanism (error detection feature) in the channel decoder. A CRC on a block of audio information bits provides this mechanism. We demonstrate how the LVA can significantly reduce the flag rate compared to the regular Viterbi algorithm (VA) for the same transmission parameters. At the expense of complexity, a receiver optional LVA can reduce the flag rate by more than an order of magnitude. The difference in audio quality is dramatic. The LVA is backward compatible with a VA.