gebhart/patrepeval huggingface dataset:
Prognostic utility of fluorescence in situ hybridization for determining HER2 gene amplification in breast cancer (2008)

An accurate investigation of the HER2 proto-oncogene is extremely important for the therapy and prognostication of breast cancer. Currently, immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) are standard methods for this purpose. The aim of this study was to detect the expression and amplification of HER2 in paraffin-embedded samples of breast cancer tissue and to investigate the relationship between HER2 amplification and various clinicopathological parameters in advanced breast cancers. We used FISH to examine the HER2 gene amplification and IHC to examine the expression of HER2 protein, estrogen receptor (ER) and progesterone receptor (PR) in 62 advanced breast cancers. HER2 gene amplification was detected by FISH in 12 breast cancers (19%) and HER2 protein expression with a score of 3+ was detected by IHC in 11 (17%). There was a significant correlation between the HER2 gene amplification and HER2 protein overexpression in breast cancers (P<0.0001). However, some mismatching was evident: 3 cases, negative for the HER2 gene, showed a HER2 protein expression score of 3+ and 2 cases, positive for HER2 gene amplification, had HER2 protein expression scores of 0 and 1+ (negative), respectively. ER and PR were expressed in 41 (66%) and 46 (74%) cancers, respectively. No correlation was observed between the HER2 gene amplification and any of the clinicopathological parameters examined, including age, histopathological type, TNM stage, tumor size, lymph node status, relapse and expression of PR. We observed three patterns among the 6 deceased cases: i) triple negativity for HER2, ER and PR, ii) positivity for HER2 gene amplification with a mismatching HER2 protein expression, and iii) positivity for the HER2 gene amplification with a matching HER2 protein expression score of 2+ or 3+. The triple negative cases and HER2 gene amplification positive cases with a mismatching HER2 protein expression had a poor outcome. These results suggest that in breast cancer, the detection of HER2 gene amplification by FISH is desirable compared with the HER2 protein expression determined by IHC. Moreover, triple negativity for HER2, ER and PR is a potentially very important prognostic marker.
Allosteric energy at the hemoglobin beta chain C terminus studied by hydrogen exchange (1988)

When hemoglobin switches from the deoxy (T) to the liganded (R) form, several of its peptide group NH experience a great increase in their rate of exchange with water. Selective labeling and fragment isolation experiments identify some of the sensitive protons as three to four near-neighbor H-bonded peptide NH placed between Ala140 beta and the C-terminal His146 beta residue. These NH have differing solvent accessibilities, yet all exchange at about the same rate, and they maintain a common rate in the face of modifications that change their exchange rate over a 1000-fold range. This suggests that their exchange is mediated by a concerted transient unfolding reaction. The removal of allosterically important salt links at the distant alpha subunit N termini (des-Arg141 alpha hemoglobin) has little if any effect on the indicator NH at the beta C terminus. This demonstrates the restricted reach of the separate allosteric interactions in the T form as well as the localized nature of the H-exchange probe. Breakage of a salt link at the beta chain C terminus (His146 beta to Asp94 beta) by chemical modification (NES-Cys93 beta hemoglobin) speeds exchange of the indicator peptide NH in T-state hemoglobin by six-fold, which corresponds to an allosteric destabilization at the C-terminal segment of 1 kcal (pH 7.4, 0 degrees C), according to local unfolding theory. This is in quantitative agreement with energy values obtainable from other measurements. These NH exchange with an average halftime of five hours in deoxy hemoglobin and 15 seconds in oxy hemoglobin. According to the unfolding model for protein H-exchange, the 1200-fold increase in rate indicates a loss of 3.8 kcal in structural stabilization free energy at or near the C terminus of each beta chain in the T to R transition (pH 7.4, 0 degrees C, with 2,3-diphosphoglycerate). This result together with other available data places about 70% of hemoglobin's total allosterically significant structural energy change at the beta chain C termini.
The α-bungarotoxin binding site on the nicotinic acetylcholine receptor: Analysis using a phage–epitope library (1997)

The nicotinic acetylcholine receptor (AcChoR) is a ligand-gated ion channel that is activated upon binding of acetylcholine. alpha-Neurotoxins, in particular alpha-bungarotoxin (alpha-BTX), bind specifically and with high affinity to the AcChoR and compete with binding of the natural ligand. We employed a 15-mer phage-display peptide library to select epitopes reacting with alpha-BTX. Phages bearing the motif YYXSSL as a consensus sequence were found to bind with high affinity to alpha-BTX. The library-derived peptide (MRYYESSLKSYPD) bears amino acid sequence similarities to a region of the alpha-subunit of the Torpedo muscle AcChoR, as well as of other muscle and neuronal AcChoRs that bind alpha-BTX. The library-derived peptide and the corresponding peptides containing residues 187-199 of the Torpedo AcChoR alpha-subunit (WVYYTCCPDTPYL), as well as peptides analogous to the above region in the neuronal AcChoR (e.g., human alpha7; ERFYECCKEPYPD) that binds alpha-BTX, inhibit the binding of alpha-BTX to the intact Torpedo AcChoR with IC50 values of 10(-6) M. A synthetic peptide from a neuronal AcChoR that does not bind alpha-BTX (e.g., human alpha2; ERKYECCKEPYPD) which differs by just one amino acid from the homologous peptide from the alpha-BTX-binding protein (alpha7)-i.e., Lys in alpha2 and Tyr in alpha7-does not inhibit the binding of alpha-BTX to Torpedo AcChoR. These results indicate the requirement for two adjacent aromatic amino acid residues for binding to alpha-BTX.
Differential Pulsed Voltammetric Determination of RNA at the Picomole Level in the Presence of DNA and Nucleic Acid Components (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDifferential Pulsed Voltammetric Determination of RNA at the Picomole Level in the Presence of DNA and Nucleic Acid ComponentsEmil. Palecek and Miroslav. FojtaCite this: Anal. Chem. 1994, 66, 9, 1566–1571Publication Date (Print):April 1, 1994Publication History Published online1 May 2002Published inissue 1 April 1994https://pubs.acs.org/doi/10.1021/ac00081a033https://doi.org/10.1021/ac00081a033research-articleACS PublicationsRequest reuse permissionsArticle Views216Altmetric-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 Get e-Alerts
A new lactobacilli<i>in vivo</i>expression system for the production and delivery of heterologous proteins at mucosal surfaces (2016)

Food-grade lactic acid bacteria, such as lactobacilli, represent good candidates for the development of mucosal vectors. Indeed, they are generally recognized as safe microorganisms and some strains display beneficial effects (probiotics). In this study, we described a new lactobacilli in vivo expression (LIVE) system for the production and delivery of therapeutic molecules at mucosal surfaces. The versatility and functionality of this system was successfully validated in several lactobacilli species; furthermore, we assessed in vivo LIVE system in two different mouse models of human pathologies: (i) a model of therapy against intestinal inflammation (inflammatory bowel diseases) and (ii) a model of vaccination against dental caries. We demonstrated that Lactobacillus gasseri expressing the anti-inflammatory cytokine IL-10 under LIVE system efficiently delivered the recombinant protein at mucosal surfaces and display anti-inflammatory effects. In the vaccination model against caries, LIVE system allowed the heterologous expression of Streptococcus mutans antigen GbpB by L. gasseri, leading to a stimulation of the host immune response.
<title>AMLCD design considerations for avionics and vetronics applications</title> (1998)

There is significant debate concerning the use of ruggedized consumer or commercial off the shelf (COTS) displays in avionics and ground vehicle applications. The environmental, life cycle, and optical performance data comparing ruggedized and custom displays is limited. The main purpose of this paper is to discuss which product design aspects and components must be considered when implementing active matrix liquid crystal display (AMLCD) technology in avionics and vetronics applications. The focus will be on which aspects of the AMLCD design can and cannot be ruggedized or modified to improve environmental or optical performance. In addition, preliminary environmental data will be presented comparing consumer, ruggedized consumer, and custom displays. Finally, a test plan for complete environmental and optical data comparison of ruggedized versus custom will be discussed. This paper will not address physical characteristics, full optical performance, or life cycle cost issues with ruggedized AMLCDs.
Properties of the amphoteric, thermally regenerable ion-exchange resins Amberlite XD-2 and Amberlite XD-5 (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTProperties of the amphoteric, thermally regenerable ion-exchange resins Amberlite XD-2 and Amberlite XD-5Tah-Ben Hsu and Robert L. PigfordCite this: Ind. Eng. Chem. Prod. Res. Dev. 1981, 20, 2, 361–365Publication Date (Print):June 1, 1981Publication History Published online1 May 2002Published inissue 1 June 1981https://pubs.acs.org/doi/10.1021/i300002a025https://doi.org/10.1021/i300002a025research-articleACS PublicationsRequest reuse permissionsArticle Views120Altmetric-Citations1LEARN 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 options Get e-Alerts
Learning from one example through shared densities on transforms (2002)

We define a process called congealing in which elements of a dataset (images) are brought into correspondence with each other jointly, producing a data-defined model. It is based upon minimizing the summed component-wise (pixel-wise) entropies over a continuous set of transforms on the data. One of the biproducts of this minimization is a set of transform, one associated with each original training sample. We then demonstrate a procedure for effectively bringing test data into correspondence with the data-defined model produced in the congealing process. Subsequently; we develop a probability density over the set of transforms that arose from the congealing process. We suggest that this density over transforms may be shared by many classes, and demonstrate how using this density as "prior knowledge" can be used to develop a classifier based on only a single training example for each class.
A prospective, randomized trial of gauze and two polyurethane dressings for site care of pulmonary artery catheters: Implications for catheter management (1994)

The incidence of pulmonary artery catheter-related bloodstream infection has decreased over the past 5 yrs. Pulmonary artery catheter-related bloodstream infections originate from multiple sources, indicating that measures to prevent bacteremic infections of these devices must focus both on reducing cutaneous colonization at the insertion site and averting contamination of infusate and catheter hubs. Efforts should be made to limit the duration of catheterization with pulmonary artery catheters (including the introducer) to no longer than 4 days. The polyurethane dressings studied appear to be safe for use with pulmonary artery catheters and may be left on for up to 5 days between dressing changes.
Intravenous gamma-globulin in infant acquired immunodeficiency syndrome (1986)

From the Departments of Pediatrics and Microbiology and Immunology, the Albert Einstein College of Medicine, Bronx, NY.
Directed <i>ortho </i>Metalation-Based Methodology. Halo-, Nitroso-, and Boro-Induced <i>i</i><i>pso-</i>Desilylation. Link to an <i>in </i><i>s</i><i>itu</i> Suzuki Reaction (2006)

ADVERTISEMENT RETURN TO ISSUEPREVAdditions & Corr...Additions & CorrectionsORIGINAL ARTICLEThis notice is a correctionDirected ortho Metalation-Based Methodology. Halo-, Nitroso-, and Boro-Induced ipso-Desilylation. Link to an in situ Suzuki ReactionZhongdong Zhao and Victor SnieckusCite this: Org. Lett. 2006, 8, 18, 4173Publication Date (Web):August 1, 2006Publication History Published online1 August 2006Published inissue 1 August 2006https://pubs.acs.org/doi/10.1021/ol061787mhttps://doi.org/10.1021/ol061787mcorrectionACS PublicationsCopyright © 2006 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views794Altmetric-Citations1LEARN 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 PDF (6 KB) Get e-AlertscloseSUBJECTS:Chemical structure,Nuclear magnetic resonance spectroscopy,Purification,Solvents Get e-Alerts
Glucose Transporter of <i>Escherichia coli</i>:  NMR Characterization of the Phosphocysteine Form of the IIB<sup>Glc</sup> Domain and Its Binding Interface with the IIA<sup>Glc</sup> Subunit (1997)

The transmembrane subunit of the glucose transporter, IICB(Glc), mediates vectorial transport with concomitant phosphorylation of glucose. Glucose phosphorylation proceeds through a cystein phosphate intermediate of the cytosolic IIB domain of IIC(Glc), which is phosphorylated by the IIA(Glc) subunit of the glucose transporter. Two- and three-dimensional NMR experiments were used to characterize the phosphorylation of the 10 kDa subclonal IIB domain and the complementary binding interfaces of [15N]IIB and [15N]IIA(Glc). The largest chemical shift perturbations and the only NOE differences accompanying IIB phosphorylation are confined to the active site residue Cys35, as well as Ile36, Thr37, Arg38, Leu39, and Arg40, which are all located in the turn between strands beta1 and beta2 and on beta2 itself. The significant increase of the amide cross-peak intensities of Ile36, Thr37, and Arg38 upon phosphorylation suggests that the conformational freedom of these groups becomes restrained, possibly due to hydrogen bonding to the oxygens of the bound phosphate and to interactions between the guanidinium group of Arg38 and the phosphoryl group. The residues of IIB which experience chemical shift perturbations upon binding of IIA are located on a protruding surface formed by residues of strands beta1, beta2, and beta4, the beta4/alpha3 loop, and residues from the first two turns of alpha3. The corresponding binding surface of the IIA(Glc) domain is comprised of residues on five adjacent beta-strands and two short helices surrounding the active site His90. The binding surface of IIA(Glc) for IIB coincides with the binding surface for HPr, the phosphoryl carrier protein by which IIA(Glc) is phosphorylated [Chen, Y., Reizer, J., Saier, M. H., Fairbrother, W. J., & Wright, P. E. (1993) Biochemistry 32, 32-37].
Casein Kinase Iε Modulates the Signaling Specificities of Dishevelled (2004)

Wnt signaling is critical to many aspects of development, and aberrant activation of the Wnt signaling pathway can cause cancer. Dishevelled (Dvl) protein plays a central role in this pathway by transducing the signal from the Wnt receptor complex to the beta-catenin destruction complex. Dvl also plays a pivotal role in the planar cell polarity pathway that involves the c-Jun N-terminal kinase (JNK). How functions of Dvl are regulated in these two distinct pathways is not clear. We show that deleting the C-terminal two-thirds of Dvl, which includes the PDZ and DEP domains and is essential for Dvl-induced JNK activation, rendered the molecule a much more potent activator of the beta-catenin pathway. We also found that casein kinase Iepsilon (CKIepsilon), a previously identified positive regulator of Wnt signaling, stimulated Dvl activity in the Wnt pathway, but dramatically inhibited Dvl activity in the JNK pathway. Consistent with this, overexpression of CKIepsilon in Drosophila melanogaster stimulated Wnt signaling and disrupted planar cell polarity. We also observed a correlation between the localization and the signaling activity of Dvl in the beta-catenin pathway and the JNK pathway. Furthermore, by using RNA interference, we demonstrate that the Drosophila CKIepsilon homologue Double time positively regulates the beta-catenin pathway through Dvl and negatively regulates the Dvl-induced JNK pathway. We suggest that CKIepsilon functions as a molecular switch to direct Dvl from the JNK pathway to the beta-catenin pathway, possibly by altering the conformation of the C terminus of Dvl.
Class-Specific Feature Selection for One-Against-All Multiclass SVMs (2011)

This paper proposes a method to perform class-specic fea- ture selection in multiclass support vector machines addressed with the one-against-all strategy. The main issue arises at the nal step of the classication process, where binary classier outputs must be compared one against another to elect the winning class. This comparison may be biased towards one specic class when the binary classiers are built on distinct feature subsets. This paper proposes a normalization of the binary classiers outputs that allows fair comparisons in such cases.
Thrombin Receptor Occupancy Modulates Aggregation Efficiency and Platelet Surface Expression of vWF and Thrombospondin at Low Thrombin Concentrations (1999)

Previous studies evaluating requirements for occupancy of thrombin receptors in normal platelet secretion and aggregation, using the thrombin antagonists hirudin and PPACK (D-Phe-Pro-Arg-chloromethylketone), have suggested that at low thrombin activating concentrations (0.025-0.13 U/ml), occupancy was required only in the first 45-60 s following activation. In our study, we differentiate between thrombin receptor occupancy requirements for surface expression of secreted adhesive proteins, for activation of GPIIb-IIIa receptors, and for aggregation of washed platelets (WP) in laminar shear flow. Platelets activated with 0.05 U/ml thrombin for 10 min to allow maximal secretion (hereafter referred to as "pre-activated platelets"), then sheared, showed a 50-70% decrease in platelet counts after 60 s of shear. Treatment of pre-activated platelets with hirudin or PPACK produced a 65% reduction of capture efficiencies, alphaG (reflecting experimental/theoretical initial rates of aggregation), as well as a 30-40% decrease in the surface expression of von Willebrand factor (vWF) and thrombospondin (TSP). However, alpha-granule membrane P-selectin expression and numbers of activated GPIIb-IIIa receptors were comparable for treated and non-treated platelets. No significant difference in any of the parameters tested was observed when platelets were similarly pre-activated with 0.2 U/ml thrombin, due to treatment with thrombin antagonists. Binding of soluble FITC-vWF (GRGDSP-sensitive) to pre-activated, thrombin antagonist treated platelets, was greatly reduced (> or =80%). Soluble Fg was shown to bind to antagonist-treated pre-activated platelets, but could not significantly enhance platelet aggregation. Although occupancy of thrombin receptors by catalytically active thrombin is required transiently for secretion and activation of platelets, there is a further requirement for thrombin occupancy at low thrombin concentrations, for optimizing initial rates of platelet aggregation, surface expression of vWF and TSP, and activated GPIIb-IIIa ligand recognition.
Experimental investigation and thermodynamic calculation of the Fe–Mg–Mn and Fe–Mg–Ni systems (2011)

Abstract Based on the thermodynamic calculations extrapolated from the corresponding binary sub-systems, four decisive alloys in the Fe–Mg–Mn system and three in the Fe–Mg–Ni system were selected and prepared using a powder metallurgy method to measure the isothermal sections at 500 8C in both systems. The prepared samples were annealed at 5008C, and then subjected to X-ray diffraction, optical microscopy, scanning electron microscopy with energy-dispersive X-ray spectrometry as well as electron probe microanalysis. Taking into account the presently obtained experimental data and the experimental data available in the literature, thermodynamic modeling was performed for the above systems. It was found that a direct extrapolation from the corresponding three binary systems can well reproduce all the experimental data in the Fe–Mg–Mn system, while two thermodynamic parameters are needed in the Fe–Mg–Ni system to fit all the experimental data. The liquidus projections and reaction schemes for the Fe–Mg–Mn and Fe–Mg–Ni systems are also presented.