gebhart/patrepeval huggingface dataset:
Intracellular localization of mesothelin predicts patient prognosis of extrahepatic bile duct cancer (2012)

Mesothelin is expressed in various types of malignant tumors, and we recently reported that the expression of mesothelin was related to unfavorable patient outcome in pancreatic ductal adenocarcinoma and gastric adenocarcinoma. In this study, we examined the clinicopathological significance of mesothelin expression in extrahepatic bile duct cancer (EHBDCA), especially in terms of its association with the staining pattern. Tissue samples from 61 EHBDCA (16 hilar cholangiocarcinoma, 17 upper bile duct adenocarci-noma, 20 middle bile duct adenocarcinoma and 8 distal bile duct adenocarcinoma) were immunohistochemically examined. The expression levels of mesothelin in tumor cells was classified into the localization of mesothelin in luminal membrane and/or cytoplasm, in addition to high and low according to the staining intensity and proportion as a conventional analysis. 'High-level expression' of mesothelin (47.5%) was statistically correlated with liver metastasis (P=0.013) and poorer patient outcome (P=0.022), while 'luminal membrane positive' of mesothelin (52.5%) was more significantly correlated with liver metastasis (P=0.006), peritoneal metastasis (P=0.024) and unfavorable patient outcome (P=0.017). Moreover, we found that 'cytoplasmic expression' isolated from 'luminal membrane negative' of mesothelin represented the best patient prognosis throughout this study. We describe the expression pattern level of mesothelin, i.e., in luminal membrane or cytoplasm both high and low level, evidently indicate the patient prognosis of EHBDCA, suggesting the pivotal role of mesothelin in cancer promotion depending on its intracellular localization.
Fcγ Receptor IIB on Dendritic Cells Enforces Peripheral Tolerance by Inhibiting Effector T Cell Responses (2007)

The uptake of immune complexes by FcRs on APCs augments humoral and cellular responses to exogenous Ag. In this study, CD11c+ dendritic cells are shown to be responsible in vivo for immune complex-triggered priming of T cells. We examine the consequence of Ab-mediated uptake of self Ag by dendritic cells in the rat insulin promoter-membrane OVA model and identify a role for the inhibitory FcgammaRIIB in the maintenance of peripheral CD8 T cell tolerance. Effector differentiation of diabetogenic OT-I CD8+ T cells is enhanced in rat insulin promoter-membrane OVA mice lacking FcgammaRIIB, resulting in a high incidence of diabetes. FcgammaRIIB-mediated inhibition of CD8 T cell priming results from suppression of both DC activation and cross-presentation through activating FcgammaRs. Further FcgammaRIIB on DCs inhibited the induction of OVA-specific Th1 effectors, limiting Th1-type differentiation and memory T cell accumulation. In these MHC II-restricted responses, the presence of FcgammaRIIB only modestly affected initial CD4 T cell proliferative responses, suggesting that FcgammaRIIB limited effector cell differentiation primarily by inhibiting DC activation. Thus, FcgammaRIIB can contribute to peripheral tolerance maintenance by inhibiting DC activation alone or by also limiting processing of exogenously acquired Ag.
Structure and energetics of the vacancy in graphite (2003)

We determine properties of the vacancy in graphite from first principles calculations. The ground-state structure is associated with a formation energy of 7.4 eV and arises through a combination of symmetric relaxation and symmetry-breaking Jahn-Teller distortion to one of three degenerate, symmetry-related structures. The distortion results in a weak reconstructed bond and small out-of-plane atomic displacements. Dynamic switching between degenerate structures is activated by a barrier of 0.1 eV and we interpret scanning tunneling microscopy observations on the basis of thermal averaging between structures. The calculated migration energy of 1.7 eV is lower than that widely accepted from experiment, and we propose that the discrepancy is explained by a revised picture of trapping during vacancy transport, dependent on concentration. We discuss the significance of these findings in understanding defect behavior in irradiated graphite and related graphitic materials, in particular single-walled nanotubes.
C4d Detection in Renal Allograft Biopsies: Immunohistochemistry vs. Immunofluorescence (2012)

Introduction. Peritubular capillary complement 4d staining is one of the criteria for the diagnosis of antibody-mediated rejection, and research into this is essential to kidney allograft evaluation. The immunofluorescence technique applied to frozen sections is the present gold-standard method for complement 4d staining and is used routinely in our laboratory. The immunohistochemistry technique applied to paraffin-embedded tissue may be used when no frozen tissue is available. Material and Methods.The aim of this study is to evaluate the sensitivity and specificity of immunohistochemistry compared with immunofluorescence. We describe the advantages and disadvantages of the immunohistochemistry vs. the immunofluorescence technique. For this purpose complement 4d staining was performed retrospectively by the two methods in indication biopsies (n=143) and graded using the Banff 07 classification. Results.There was total classification agreement between methods in 87.4% (125/143) of cases. However, immunohistochemistry staining caused more difficulties in interpretation, due to nonspecific staining in tubular cells and surrounding interstitium. All cases negative by immunofluorescence were also negative by immunohistochemistry. The biopsies were classified as positive in 44.7% (64/143) of cases performed byimmunofluorescence vs. 36.4% (52/143) performed by immunohistochemistry. Fewer biopsies were classified as positive diffuse in the immunohistochemistry group (25.1% vs. 31.4%) and more as positive focal (13.2% vs. 11.1%). More cases were classified as negative by immunohistochemistry (63.6% vs. 55.2%). Study by ROC curve showed immunohistochemistry has a specificity of 100% and a sensitivity of 81.2% in relation to immunofluorescence (AUC: 0.906; 95% confidence interval: 0.846-0.949; p=0.0001). Conclusions.The immunohistochemistry method presents an excellent specificity but lower sensitivity to C4d detection in allograft dysfunction. The evaluation is more difficult, requiring a more experienced observer than the immunofluorescence method. Based on these results, we conclude that the immunohistochemistry technique can safely be used when immunofluorescence is not available
Determination of the non-ionic detergent insolubility and phosphoprotein associations of glycosylphosphatidylinositol-anchored proteins expressed on T cells (1998)

Glycosylphosphatidylinositol (GPI)-anchored proteins are poorly solublized in non-ionic detergents such as Triton X-100 and Nonidet P40, but are easily solublized by detergents with high critical micelle concentrations such as octylglucoside. This solubility profile has been suggested to be due to the localization of GPI-anchored proteins to lipid microdomains rich in cholesterol and sphingolipids. Additionally, GPI-anchored proteins expressed on haemopoietic cells have been shown to associate with src-family tyrosine kinases and heterotrimeric G proteins. Despite these observations, the non-ionic detergent insolubility of GPI-anchored proteins on haemopoietic cells has not been quantified nor has a relationship between the non-ionic detergent insolubility of these proteins and their association with signal-transduction molecules been identified. Here we show that GPI-anchored proteins found on T-cell tumours and activated T cells, although significantly more insoluble then transmembrane proteins, are not uniform in their detergent insolubility. Whereas CD59 was between 4% and 13% soluble, CD48 was between 13% and 25% soluble, CD55 was between 20% and 30% soluble, and CD109 was between 34% and 75% soluble. The ability of these GPI-anchored proteins to associate with phosphoproteins was correlated with their detergent insolubility: the more detergent-insoluble that a GPI-anchored protein was, the greater the level of phosphoprotein associations. These experiments reveal a relationship between non-ionic detergent insolubility and association with signal-transduction molecules and suggest a cause-and-effect relationship between these two properties. In total, these experiments support the hypothesis that the association of GPI-anchored proteins with signalling molecules is due to their sorting to lipid microdomains.
Activation of collagen IV gene expression in F9 teratocarcinoma cells by 3-deazaadenosine analogs. Indirect inhibitors of methylation. (1992)

3-Deazaadenosine analogs can function as inhibitors and also as alternative substrates of S-adenosylhomocysteine (AdoHcy) hydrolase. In cells treated with the analogs, AdoHcy invariably accumulates, leading to inhibition of cellular methylation. F9 teratocarcinoma cells, stably transfected with two collagen (IV) promoter-enhancer-CAT constructs and treated with 10 microM 3-deazaadenosine, 3-deaza-(+-)-aristeromycin or 3-deazaneplanocin, showed a strong induction of CAT activities without affecting differentiation. In comparison, the same 3-deaza analogs did not affect the CAT activity in F9 cells transfected with the beta-actin promoter-CAT construct. Furthermore, Northern blot analysis of endogenous mRNA from wild-type F9 cells treated with the 3-deaza nucleosides all showed an induction of the collagen alpha 1(IV) chain mRNA. Thus, the 3-deaza analogs most likely affect DNA methylation because their results are consistent with the previous observation that the integrated collagen alpha 1(IV) promoter-enhancer constructs were activated with 5-azacytidine.
On‐column conductivity detection in capillary‐chip electrophoresis (2007)

On-column conductivity detection in capillary-chip electrophoresis was achieved by actively coupling the high electric field with two sensing electrodes connected to the main capillary channel through two side detection channels. The principle of this concept was demonstrated by using a glass chip with a separation channel incorporating two double-Ts. One double-T was used for sample introduction, and the other for detection. The two electrophoresis electrodes apply the high voltage and provide the current, and the two sensing electrodes connected to the separation channel through the second double-T and probe a potential difference. This potential difference is directly related to the local resistance or the conductivity of the solution defined by the two side channels on the main separation channel. A detection limit of 15 microM (600 ppb or 900 fg) was achieved for potassium ion in a 2 mM Tris-HCl buffer (pH 8.7) with a linear range of 2 orders of magnitude without any stacking. The proposed detection method avoids integrating the sensing electrodes directly within the separation channel and prevents any direct contact of the electrodes with the sample. The baseline signal can also be used for online monitoring of the electric field strength and electroosmosis mobility characterization in the separation channel.
Central Sleep Apnea and Cheyne-Stokes Respiration (2008)

Cheyne-Stokes respiration with central sleep apnea (CSR-CSA) is a form of periodic breathing, commonly observed in patients with heart failure (HF), in which central apneas alternate with hyperpneas that have a waxing-waning pattern of tidal volume. Uniform criteria by which to diagnose a clinically significant degree of CSR-CSA have yet to be established. CSR-CSA is caused by respiratory control system instability characterized by a tendency to hyperventilate. Central apnea occurs when Pa(CO(2)) falls below the threshold for apnea during sleep due to ventilatory overshoot. Patients with CSR-CSA are generally hypocapnic, with a Pa(CO(2)) closer than normal to the apneic threshold such that even slight augmentation in ventilation drives Pa(CO(2)) below threshold and triggers apnea. Factors contributing to hyperventilation in HF include stimulation of pulmonary irritant receptors by pulmonary congestion, increased chemoreceptor sensitivity, reduced cerebrovascular blood flow, and recurrent arousals from sleep. Controversy remains as to whether CSR-CSA is simply a reflection of HF severity, or whether it exerts unique adverse effects on prognosis. The main adverse influence of CSR-CSA on cardiovascular function appears to be excessive sympathetic nervous system activity due to apnea-related hypoxia and arousals from sleep. A number of studies have examined the potential relationship between CSR-CSA and mortality in HF. Most reported that CSR-CSA was associated with an increased risk for mortality, but these studies were small. Further research is therefore needed to elucidate mechanisms which contribute to the pathogenesis of CSR-CSA, and to determine whether its treatment can reduce morbidity and mortality in patients with HF.
Design of omnimobile robot wheels (2002)

Typical mobile robot structures (e.g. wheelchair or car-like) do not have the required mobility for common applications such as displacement in a corridor, hospital and office. New structures based on the "universal wheel" (i.e. a wheel equipped with free rotating rollers) have been developed to increase mobility. However these structures have important drawbacks such as vertical vibration and limited load capacity. This paper presents a comparison of several types of universal wheel performances based on the three following criteria: load capacity, surmountable bumps and vertical vibration. It is hoped that this comparison will help the designer in the selection of the best suitable solution for his/her application.
Lymph node metastases from glioblastoma multiforme. (1997)

Extraneural metastases from glioblastoma multiforme are rare. Spread to the extracranial head and neck may be evident on routine follow-up images of the original lesion. We present two cases, one with documented metastatic adenopathy in the head and neck from glioblastoma and the other with probable metastatic disease in a lymph node in which biopsy was not performed, and discuss probable mechanisms of extraneural extension of this tumor.
Preservation of Influenza Virus Infectivity by Lyophilization (1968)

A method of lyophilizing influenza virus in allantoic fluid with retention of high-titer of egg infectivity is described. Five strains of virus were lyophilized, and all were much more stable than fluid virus preparations, retaining 2 to 3 logs of infectivity after storage at 37 C for 60 to 95 days. Statistical analysis of an accelerated storage test by extrapolation of viral degradation indicates that the lyophilized viruses are stable indefinitely at or below room temperature.
Clinical Trials in Radiotherapy and the Merits of High Energy Protons (1970)

(1970). Clinical Trials in Radiotherapy and the Merits of High Energy Protons. Acta Radiologica: Therapy, Physics, Biology: Vol. 9, No. 1, pp. 1-23.
Positive Effects of Glucocorticoids on T Cell Function by Up-Regulation of IL-7 Receptor α (2002)

Despite the effects of glucocorticoids on immune function, relatively little is known about glucocorticoid-inducible genes and how their products may regulate lymphocyte function. Using DNA microarray technology to analyze gene expression in PBMC from healthy donors, we identified IL-7Ralpha as a glucocorticoid-inducible gene. This observation was confirmed at the mRNA and protein levels. Conversely, TCR signaling decreased IL-7Ralpha expression, and the relative strength of signaling between these two receptors determined the final IL-7Ralpha levels. The up-regulation of IL-7Ralpha by glucocorticoids was associated with enhanced IL-7-mediated signaling and function. Moreover, IL-7-mediated inhibition of apoptosis at increasing concentrations of glucocorticoids is consistent with enhanced cell sensitivity to IL-7 following glucocorticoid exposure. These observations provide a mechanism by which glucocorticoids may have a positive influence on T cell survival and function.
Exosomes From Human CD34 + Stem Cells Mediate Their Proangiogenic Paracrine Activity (2011)

Our data demonstrate that human CD34(+) cells secrete exosomes that have independent angiogenic activity both in vitro and in vivo. CD34(+) exosomes may represent a significant component of the paracrine effect of progenitor cell transplantation for therapeutic angiogenesis.
Construction of synthetic macrocyclic compounds possessing subheterocyclic rings, specifically pyridine, furan, and thiophene (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTConstruction of synthetic macrocyclic compounds possessing subheterocyclic rings, specifically pyridine, furan, and thiopheneGeorge R. Newkome, Joe D. Sauer, Jerry M. Roper, and David C. HagerCite this: Chem. Rev. 1977, 77, 4, 513–597Publication Date (Print):August 1, 1977Publication History Published online1 May 2002Published inissue 1 August 1977https://pubs.acs.org/doi/10.1021/cr60308a003https://doi.org/10.1021/cr60308a003research-articleACS PublicationsRequest reuse permissionsArticle Views1436Altmetric-Citations161LEARN 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
Highly specific ubiquitin-competing molecules effectively promote frataxin accumulation and partially rescue the aconitase defect in Friedreich ataxia cells (2014)

Friedreich ataxia is an inherited neurodegenerative disease that leads to progressive disability. There is currently no effective treatment and patients die prematurely. The underlying genetic defect leads to reduced expression of the mitochondrial protein frataxin. Frataxin insufficiency causes mitochondrial dysfunction and ultimately cell death, particularly in peripheral sensory ganglia. There is an inverse correlation between the amount of residual frataxin and the severity of disease progression; therefore, therapeutic approaches aiming at increasing frataxin levels are expected to improve patients' conditions. We previously discovered that a significant amount of frataxin precursor is degraded by the ubiquitin/proteasome system before its functional mitochondrial maturation. We also provided evidence for the therapeutic potential of small molecules that increase frataxin levels by docking on the frataxin ubiquitination site, thus preventing frataxin ubiquitination and degradation. We called these compounds ubiquitin-competing molecules (UCM). By extending our search for effective UCM, we identified a set of new and more potent compounds that more efficiently promote frataxin accumulation. Here we show that these compounds directly interact with frataxin and prevent its ubiquitination. Interestingly, these UCM are not effective on the ubiquitin-resistant frataxin mutant, indicating their specific action on preventing frataxin ubiquitination. Most importantly, these compounds are able to promote frataxin accumulation and aconitase rescue in cells derived from patients, strongly supporting their therapeutic potential.
The use of atomic force microscopy for the observation of corneal epithelium surface. (2000)

In this work the AFM parameters appropriate for corneal epithelium imaging in physiological medium were defined. AFM represents a new powerful tool for corneal epithelium imaging, and its application in this field warrants further investigation.
The flavor problem of soybean oil. VIII. Linolenic acid (1951)

Summary Circumstantial evidence has long pointed to linolenic acid as the unstable precursor of “reversion” flavors in soybean oil. Direct evidence has now been obtained from two sources: a) A qualitative study of the flavors after storage of soybean oil in which the linolenic acid content has been significantly lowered by furfural extraction, and b) organoleptic identification studies of stored soybean oil, stored cottonseed oil, and a cottonseed oil into whose glyceride structure linolenic acid has been introduced with the use of an interesterification catalyst. It is concluded that linolenic acid is an unstable precursor of “fishy‐painty‐grassy‐melony” flavors in soybean oil.
Introduction to digital signal processing and filter design (2006)

Preface. 1. Introduction. 1.1 Introduction. 1.2 Application of DSP. 1.3 Discrete-Time Signals. 1.4 History of Filter Design. 1.5 Analog and Digital Signal Processing. 1.6 Summary. Problems. References. 2. Time-Domain Analysis and z Transform. 2.1 A Linear, Time-Invariant System. 2.2 z Transform Theory. 2.3 Using z Transform to Solve Difference Equations. 2.4 Solving Difference Equations Using the Classical Method. 2.5 z Transform Method Revisited. 2.6 Convolution Revisited. 2.7 A Model from Other Models. 2.8 Stability. 2.9 Solution Using MATLAB Functions. 2.10 Summary. Problems. References. 3. Frequency-Domain Analysis. 3.1 Introduction. 3.2 Theory of Sampling. 3.3 DTFT and IDTFT. 3.4 DTFT of Unit Step Sequence. 3.5 Use of MATLAB to Compute DTFT. 3.6 DTFS and DFT. 3.7 Fast Fourier Transform. 3.8 Use of MATLAB to Compute DFT and IDFT. 3.9 Summary/ Problems. References. 4. Infinite Impulse Response Filters. 4.1 Introduction. 4.2 Magnitude Approximation of Analog Filters. 4.3 Analog Frequency Transformations. 4.4 Digital Filters. 4.5 Impulse-Invariant Transformation. 4.6 Bilinear Transformation. 4.7 Digital Spectral Transformation. 4.8 Allpass Filters. 4.9 IIR Filter Design Using MATLAB. 4.10 Yule-Walker Approximation. 4.11 Summary. Problems. References. 5. Finite Impulse Response Filters. 5.1 Introduction. 5.2 Linear Phase Fir Filters. 5.3 Fourier Series Method Modified by Windows. 5.4 Design of Windowed FIR Filter Using MATLAB. 5.5 Equiripple Linear Phase FIR Filters. 5.6 Design of Equiripple FIR Filters Using MATLAB. 5.7 Frequency Sampling Method. 5.8 Summary. Problems. References. 6. Filter Realizations. 6.1 Introduction. 6.2 FIR Filter Realizations. 6.3 IIR Filter Realizations. 6.4 Allpass Filters in Parallel. 6.5 Realization of FIR and IIR Filters Using MATLAB. 6.6 Summary. Problems. References. 7. Quantized Filter Analysis. 7.1 Introduction. 7.2 Filter Design-Analysis Tool. 7.3 Quantized Filter Analysis. 7.4 Binary Numbers and Arithmetic. 7.5 Quantization Analysis of IIR Filters. 7.6 Quantization Analyis of FIR Filters. 7.7 Summary. Problems. References. 8. Hardware Design Using DSP Chips. 8.1 Introduction. 8.2 Simulink and Real-Time Workshop. 8.3 Design Preliminaries. 8.4 Code Generation. 8.5 Code Composer Studio. 8.6 Simulator and Emulator. 8.7 Conclusion. References. 9. MATLAB Primer. 9.1 Introduction. 9.2 Signal Processing Toolbox. References. Index.