gebhart/patrepeval huggingface dataset:
Phospholamban Thiols Play a Central Role in Activation of the Cardiac Muscle Sarcoplasmic Reticulum Calcium Pump by Nitroxyl (2008)

Nitroxyl (HNO) donated by Angeli's salt activates uptake of Ca(2+) by the cardiac SR Ca(2+) pump (SERCA2a). To determine whether HNO achieves this by a direct interaction with SERCA2a or its regulatory protein, phospholamban (PLN), we measured its effects on SERCA2a activation (as reflected in dephosphorylation) using insect cell microsomes expressing SERCA2a with or without PLN (wild-type and Cys --> Ala mutant). The results show that activation of SERCA2a dephosphorylation by HNO is PLN-dependent and that PLN thiols are targets for HNO. We conclude that HNO produces a disulfide bond that alters the conformation of PLN, relieving inhibition of the Ca(2+) pump.
Cancer-associated fibroblasts induce PDL1+ neutrophils through the IL6-STAT3 pathway that foster immune suppression in hepatocellular carcinoma (2018)

Emerging evidence indicate that cancer-associated fibroblasts (CAFs) affect tumor progression by reshaping the tumor microenvironment. Neutrophils are prominent components of solid tumors and important in cancer progression. Whether the phenotype and function of neutrophils in hepatocellular carcinoma (HCC) are influenced by CAFs is not well understood. Herein, we investigated the effect of HCC-derived CAFs (HCC-CAFs) on the neutrophils and explored the biological role of this effect. We found that HCC-CAFs induced chemotaxis of neutrophils and protected them from spontaneous apoptosis. Neutrophils were activated by the conditioned medium from HCC-CAFs with increased expression of CD66b, PDL1, IL8, TNFa, and CCL2, and with decreased expression of CD62L. HCC-CAF-primed neutrophils impaired T-cell function through the PD1/PDL1 signaling pathway. We revealed that HCC-CAFs induced the activation of STAT3 pathways in neutrophils, which are essential for the survival and function of activated neutrophils. In addition, we demonstrated that HCC-CAF-derived IL6 was responsible for the STAT3 activation of neutrophils. Collectively, our results suggest that HCC-CAFs regulate the survival, activation, and function of neutrophils within HCC through an IL6-STAT3-PDL1 signaling cascade, which presents a novel mechanism for the role of CAFs in remodeling the cancer niche and provides a potential target for HCC therapy.
Purification and properties of the cellular and scrapie hamster prion proteins (1988)

During scrapie infection an abnormal isoform of the prion protein (PrP), designated PrPSc, accumulates and is found to copurify with infectivity; to date, no nucleic acid has been found which is scrapie-specific. Both uninfected and scrapie-infected cells synthesize a PrP isoform, denoted PrPC, which exhibits physical properties that differentiate it from PrPSc. PrPC was purified by immunoaffinity chromatography using a PrP-specific monoclonal antibody cross-linked to protein-A--Avidgel. PrPSc was purified by detergent extraction, poly(ethylene glycol) precipitation and repeated differential centrifugation of PrPSc polymers. Both PrP isoforms were found to have the same N-terminal amino acid sequence which begins at a predicted signal peptide cleavage site. The first 8 residues of PrPC were found to be KKXPKPGG and the first 29 residues of PrPSc were found to be KKXPKPGGWNTGGSXYPGQGSPGGNRYPP. Arg residues 3 and 15 in PrPSc and 3 in PrPC appear to be modified since no detectable signals (denoted X) were found at these positions during gas-phase sequencing. Both PrP isoforms were found to contain an intramolecular disulfide bond, linking Cys 179 and 214, which creates a loop of 36 amino acids containing the two N-linked glycosylation sites. Development of a purification protocol for PrPC should facilitate comparisons of the two PrP isoforms and lead to an understanding of how PrPSc is synthesized either from PrPC or a precursor.
Relationships between Anti-Ganglioside Antibodies and Clinical Characteristics of Guillain-Barre Syndrome. (1997)

We studied relationships between anti-ganglioside antibodies and the clinical characteristics of Guillain-Barré syndrome (GBS) using multivariate analysis. Serum anti-ganglioside antibodies were measured by enzyme-linked immunosorbent assay (ELISA) in 42 GBS patients and 47 controls. Relationships between antibodies and 15 clinical characteristics were analyzed using a logistic model. Anti-GM1 antibodies were significantly infrequent in patients with objective sensory disturbance (immunoglobulin G (IgG), p < 0.05, odds ratio = 0.094; immunoglobulin M (IgM), p < 0.01, odds ratio = 0.032) and frequent in patients with prodromal diarrhea (IgG, p < 0.05, odds ratio = 5.759; IgM, p < 0.05, odds ratio = 16.28). The combination of anti-GM1 and anti-GD1b antibodies was frequent in patients with prodromal diarrhea (IgG, p < 0.01, odds ratio = 9.667; IgM, p < 0.01, odds ratio = 14.50). IgG anti-GQ1b antibodies were extremely frequent in patients with ophthalmoplegia (p < 0.01, odds ratio = 102.3), and infrequent in patients with objective sensory disturbance (p < 0.05, odds ratio = 0.023).
Pathomechanism of Pain-Related Behavior Produced by Allografts of Intervertebral Disc in the Rat (1996)

The nucleus pulposus and anulus fibrosus produce different forms of hyperalgesia (mechanical vs. thermal) associated with different and distinct immunohistochemical changes. It is possible that radicular pain of a lumbar disc herniation results from chemicals, such as phospholipase A2 and nitric oxide.
Elagolix for the management of heavy menstrual bleeding associated with uterine fibroids: results from a phase 2a proof-of-concept study (2017)

NCT01441635.
Genetic Control of the Domestication Syndrome in Common Bean (1996)

The marked pbenotypic differences for morphological and physiological traits that distinguish wild progenitors and cultivated descendants (“the domestication syndrome”) and the lack of information about their genetic control have limited the utilization of wild germplasm for crop involvement. This study was conducted to assess the genetic control of the domestication syndrome in common bean ( Phaseolus vulgaris L.). A recombinant inbred population resulting from a cross between a wild and a cultivated common bean was subjected to molecular linkage mapping and evaluation in short‐day and long‐day environments. We show that the genetic control of this syndrome in common bean involves genes that can have a large effect (&gt;25–30%) and account for a substantial part of the phenotypic variation observed (&gt;40–50%). The distribution of domestication syndrome genes appears to be concentrations in three genomic regions with a major effect on the syndrome, one of which greatly affects growth habit and phenology, the other seed dispersal and dormancy, and a third, the size of fruit and seed, all of which are important traits in determining adaptation to a cultivated environment. Whereas the influence of genetic background and environment on the expression of some traits will have to be further analyzed, our results suggest, however, that domestication of common bean could have proceeded rapidly (provided that genetic diversity and selection intensity were high) and that evolution can proceed through changes involving a few genes with large effect rather than through a gradual accumulation of changes coded by changes with small effects. They also suggest that adaptation to rapidly changing environmental conditions may involve genes with large phenotypic effects. The information presented here should lead to marker‐assisted selection experiments of introgression of additional genetic diversity into the cultivated common bean gene pool.
An improved imaging agent for malignant melanoma, based on [Nle4, D-Phe7]α-melanocyte stimulating hormone (1995)

Two compounds have been synthesized based on [Nle4,D-Phe7]alpha-melanocyte stimulating hormone (NDP-MSH) in which either one or two peptide sequences were covalently linked through their N'-termini to a single molecule of diethylenetriamine pentaacetic acid (DTPA). These two compounds (monoNDP-MSH-DTPA and bisNDP-MSH-DTPA, respectively) bound indium-111 (111In) stably and showed hormonal activity as great or greater than alpha-melanocyte stimulating hormone (alpha-MSH). Both compounds were able to target 111In to Cloudman S91 melanomas in DBA2 mice. MonoNDP-MSH-DTPA gave the highest tumour:blood and tumour:tissue ratios and showed least unspecific radioactivity in the liver and kidney. Radioscintigraphy of mice showed good tumour localization of 111In with both compounds, clear images being obtainable within 2 h of injection. Scans with monoNDP-MSH-DTPA showed some kidney and thyroid but no liver radioactivity, whereas bisNDP-MSH-DTPA gave extensive abdominal radioactivity, most of which was associated with the liver and kidneys. MonoNDP-MSH-DTPA was cleared from the tumour much less rapidly and gave more favourable tumour:blood ratios than other alpha-MSH derivatives previously investigated. It is concluded that monoNDP-MSH-DTPA offers promise as a melanoma imaging agent in man.
Binding of spermidine to transfer ribonucleic acid (1982)

The binding of spermidine to yeast tRNAPhe and Escherichia coli tRNAGlu2 at low and high ionic strength was studied by equilibrium dialysis. Once corrected for the expected Donnan effect, the binding at low ionic strength obeys the simple relationship of equivalent binding sites, and cooperative binding of spermidine to tRNA could not be detected. At low ionic strength (0.013 M Na+ ion), tRNAPhe (yeast) has 13.9 +/- 2.3 strong spermidine binding sites per molecule with Kd = 1.39 X 10(-6) M and a few weak spermidine binding sites which were inaccessible to experimentation; tRNAGlu2 (E. coli) has 14.8 +/- 1.6 strong spermidine binding sites and 4.0 +/- 0.1 weak spermidine binding sites with Kd = 1.4 X 10(-6) M and Kd = 1.23 X 10(-4) M, respectively. At high ionic strength (0.12 M monovalent cation) and 0.01 M Mg2+, tRNAPhe (yeast) has approximately 13 strong spermidine binding sites with an apparent Kd = 3.4 X 10(-3) M while the dimeric complex tRNAPhe X tRNAGlu2 has 10.4 +/- 1.2 strong spermidine binding sites per monomer with an apparent Kd = 2.0 X 10(-3) M. In the presence of increasing Na+ ion or K+ ion concentration, spermidine binding data do not fit a model for competitive binding to tRNA by monovalent cations. Rather, analysis of binding data by the Debye-Hückel approximation results in a good fit of experimental data, indicating that monovalent cations form a counterion atmosphere about tRNA, thus decreasing electrostatic interactions. On the basis of equilibrium binding analyses, it is proposed that the binding of spermidine to tRNA occurs predominantly by electrostatic forces.
Combination chemotherapy and radiation therapy in the treatment of metastatic osteogenic sarcoma (1975)

Fourteen patients with 16 metastatic ostogenic sarcoma lesions were treated with high-dose methotrexate (HDMTX) with citrovorum factor rescue (CFR), adriamycin, and pulse high-dose cyclophosphamide combined with radiation therapy. Thirteen of 16 lesions responded. Responses consisted of relief of pain (6/6 patients) in bone lesions, roentgenographic and clinical evidence of decrease in the size of the bone lesions (6/7 patients), and a decrease in the size of pulmonary metastases (2/4 patients). The 2 patients whose pulmonary metastases responded to combined therapy developed pulmonary fibrosis and pneumonitis in the treated areas 3 months after radiation therapy (RT) (1400 and 1600 rads respectively). Of two bulky primary tumors that appeared to respond, both were ultimately found to contain viable tumor; a third less bulky primary tumor appeared to respond more completely. Three smaller metastatic bone lesions that were ultimately biopsied showed no evidence of active tumor. It is concluded that: 1) combination therapy (particularly HDMTX and RT) has an additive effect in controlling osteogenic sarcoma bone lesions, but bulky primary tumors cannot be completely eradicated; 2) although synergistic in treating osteogenic sarcoma, combination therapy can produce enhanced toxicity in surrounding normal lung tissue; and 3) combination therapy is of value in the palliative treatment of metastatic lesions other than that of lung, and in the treatment of small primary bone lesions. However, experience to date does not justify the delay in surgical ablation of a primary lesion in a child who presents without metastatic disease.
Characterization of a polyvinyl alcohol-hydrogel artificial articular cartilage prepared by injection molding (2004)

We have developed a hip hemi-arthroplasty using polyvinyl alcohol-hydrogel (PVA-H) as the treatment for hip joint disorders in which the lesion is limited to the joint surface. In previous studies, we characterized the biocompatibility and the mechanical properties of PVA-H as an arthroplasty material. To fix PVA-H firmly to the bone, we have devised an implant composed of PVA-H and porous titanium fiber mesh (TFM). However, because of poor infiltration of the PVA solution into the pores of the TFM when using the low temperature crystallization method, the strength of the PVA-H-TFM interface was insufficient. Consequently, the infiltration method was improved by adopting high-pressure injection molding. With this improved method, the bonding strength of the interface increased remarkably. However, as this injection molding requires high temperature, various mechanical properties of the PVA-H might change with this treatment in comparison with the previous method. The purpose of this study was to investigate the effect of high temperature treatment on the mechanical properties of PVA-H as artificial articular cartilage, the tensile test and friction test were performed about new PVA-H. The results showed no significant mechanical deterioration of the PVA-H. This certified that the injection-molding method did not induce the change of the mechanical properties of PVA-H and indicated the potential of hemi-arthroplasty using PVA-H by this method in the future.
Vaccinia virus cores are transported on microtubules (2003)

Infection with Vaccinia virus (VV) produces several distinct virions called intracellular mature virus (IMV), intracellular enveloped virus (IEV), cell-associated enveloped virus (CEV) and extracellular enveloped virus (EEV). In this report, we have investigated how incoming virus cores derived from IMV are transported within the cell. To do this, recombinant VVs (vA5L-EGFP-N and vA5L-EGFP-C) were generated in which the A5L virus core protein was fused with the enhanced green fluorescent protein (EGFP) at the N or C terminus. These viruses were viable, induced formation of actin tails and had a plaque size similar to wild-type. Immunoblotting showed the A5L-EGFP fusion protein was present in IMV particles and immunoelectron microscopy showed that the fusion protein was incorporated into VV cores. IMV made by vA5L-EGFP-N were used to follow the location and movement of cores after infection of PtK(2) cells. Confocal microscopy showed that virus cores were stained with anti-core antibody only after they had entered the cell and, once intracellular, were negative for the IMV surface protein D8L. These cores co-localized with microtubules and moved in a stop-start manner with an average speed of 51.8 (+/-3.9) microm min(-1), consistent with microtubular movement. Treatment of cells with nocodazole or colchicine inhibited core movement, but addition of cytochalasin D did not. These data show that VV cores derived from IMV use microtubules for intracellular transport after entry.
Photoresponsive Molecular Switch to Control Chemical Fixation of CO2 (1999)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTPhotoresponsive Molecular Switch to Control Chemical Fixation of CO2Hiroshi Sugimoto, Takayuki Kimura, and Shohei InoueView Author Information Department of Industrial Chemistry, Faculty of Engineering Science University of Tokyo Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan Cite this: J. Am. Chem. Soc. 1999, 121, 10, 2325–2326Publication Date (Web):February 26, 1999Publication History Received17 November 1998Published online26 February 1999Published inissue 1 March 1999https://pubs.acs.org/doi/10.1021/ja983960ihttps://doi.org/10.1021/ja983960irapid-communicationACS PublicationsCopyright © 1999 American Chemical SocietyRequest reuse permissionsArticle Views1462Altmetric-Citations79LEARN 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 SUBJECTS:Aluminum,Electromagnetic radiation,Inorganic carbon compounds,Irradiation,Pyrroles Get e-Alerts
Overexpression of patatin‐related phospholipase AIIIδ altered plant growth and increased seed oil content in camelina (2014)

Camelina sativa is a Brassicaceae oilseed species being explored as a biofuel and industrial oil crop. A growing number of studies have indicated that the turnover of phosphatidylcholine plays an important role in the synthesis and modification of triacylglycerols. This study manipulated the expression of a patatin-related phospholipase AIIIδ (pPLAIIIδ) in camelina to determine its effect on seed oil content and plant growth. Constitutive overexpression of pPLAIIIδ under the control of the constitutive cauliflower mosaic 35S promoter resulted in a significant increase in seed oil content and a decrease in cellulose content. In addition, the content of major membrane phospholipids, phosphatidylcholine and phosphatidylethanolamine, in 35S::pPLAIIIδ plants was increased. However, these changes in 35S::pPLAIIIδ camelina were associated with shorter cell length, leaves, stems, and seed pods and a decrease in overall seed production. When pPLAIIIδ was expressed under the control of the seed specific, β-conglycinin promoter, the seed oil content was increased without compromising plant growth. The results suggest that pPLAIIIδ alters the carbon partitioning by decreasing cellulose content and increasing oil content in camelina.
Synthesis of Macroscopically Long Ropes of Well-Aligned Single-Walled Carbon Nanotubes (2000)

Ropes of aligned single-walled carbon nanotubes (SWNTs) up to 10 cm in length (see Figure) have been synthesized here by the hydrogen and argon arc discharge method. The nanotubes are characterized by SEM, TEM, and Raman scattering, and their porosity is investigated. Measurements of the properties of SWNTs can be conveniently made on these very long ropes, which should also find practical applications.
<title>Quantifying proximity and related effects in advanced wafer processes</title> (1995)

Proximity effect correction presumes that a significant proportion of CD variations observed in wafer lithography and processes can be systematically predicted from calculations made on a pattern layout prior to fabrication. Total shape variations include a portion that repeats from chip-to-chip and wafer-to-wafer, and a randomly varying portion. Repeating effects can be compensated by modifying feature shapes on the mask pattern. The project described in this report is a study to characterize the systematic shape distortions in an experimental 0.25 micrometers process. Analyses of variation are made to quantify dependencies on specific variation sources. Two-dimensional 'behavior models,' derived from characterization data measured from processed wafers, can be used to compute shape corrections for arbitrary pattern layouts. This project was undertaken in collaboration with the Hewlett Packard Research Laboratories, Palo Alto, CA.
Quantum-information processing with circuit quantum electrodynamics (2007)

We theoretically study single and two-qubit dynamics in the circuit QED architecture. We focus on the current experimental design [Wallraff et al., Nature (London) 431, 162 (2004); Schuster et al., Nature (London) 445, 515 (2007)] in which superconducting charge qubits are capacitively coupled to a single high-$Q$ superconducting coplanar resonator. In this system, logical gates are realized by driving the resonator with microwave fields. Advantages of this architecture are that it allows for multiqubit gates between non-nearest qubits and for the realization of gates in parallel, opening the possibility of fault-tolerant quantum computation with superconduting circuits. In this paper, we focus on one- and two-qubit gates that do not require moving away from the charge-degeneracy ``sweet spot.'' This is advantageous as it helps to increase the qubit dephasing time and does not require modification of the original circuit QED. However, these gates can, in some cases, be slower than those that do not use this constraint. Five types of two-qubit gates are discussed, these include gates based on virtual photons, real excitation of the resonator, and a gate based on the geometric phase. We also point out the importance of selection rules when working at the charge degeneracy point.
NID2 and HOXA9 Promoter Hypermethylation as Biomarkers for Prevention and Early Detection in Oral Cavity Squamous Cell Carcinoma Tissues and Saliva (2011)

Differentially methylated oral squamous cell carcinoma (OSCC) biomarkers, identified in vitro and validated in well-characterized surgical specimens, have shown poor clinical correlation in cohorts with different risk profiles. To overcome this lack of relevance, we used the HumanMethylation27 BeadChip, publicly available methylation and expression array data, and quantitative methylation specific PCR to uncover differential methylation in OSCC clinical samples with heterogeneous risk profiles. A two stage design consisting of discovery and prevalence screens was used to identify differential promoter methylation and deregulated pathways in patients diagnosed with OSCC and head and neck squamous cell carcinoma. Promoter methylation of KIF1A (κ = 0.64), HOXA9 (κ = 0.60), NID2 (κ = 0.60), and EDNRB (κ = 0.60) had a moderate to substantial agreement with clinical diagnosis in the discovery screen. HOXA9 had 68% sensitivity, 100% specificity, and a 0.81 Area Under the Curve (AUC). NID2 had 71% sensitivity, 100% specificity, and a 0.79 AUC. In the prevalence screen, HOXA9 (κ = 0.82) and NID2 (κ = 0.80) had an almost perfect agreement with histologic diagnosis. HOXA9 had 85% sensitivity, 97% specificity, and a 0.95 AUC. NID2 had 87% sensitivity, 95% specificity, and a 0.91 AUC. A HOXA9 and NID2 gene panel had 94% sensitivity, 97% specificity, and a 0.97 AUC. In saliva, from OSCC cases and controls, HOXA9 had 75% sensitivity, 53% specificity, and a 0.75 AUC. NID2 had 87% sensitivity, 21% specificity, and a 0.73 AUC. This phase I Biomarker Development Trial identified a panel of differentially methylated genes in normal and OSCC clinical samples from patients with heterogeneous risk profiles. This panel may be useful for early detection and cancer prevention studies.