gebhart/patrepeval huggingface dataset:
Bloodless medicine: what to do when you can't transfuse (2014)

A better understanding of risks associated with allogeneic blood transfusions (ABTs), along with a growing population of patients who do not accept transfusions, have led to the emergence of new treatment paradigms with "bloodless medicine." In this chapter, we review prior studies describing management and outcomes in patients who refuse transfusion (referred to as "bloodless patients" herein) and summarize the approaches used at our institution. Bloodless management for surgical patients includes treatment of preoperative anemia, use of autologous blood salvage, and minimizing blood loss with procedures. Other adjuncts for both medical and surgical patients include minimizing blood loss from laboratory testing using pediatric phlebotomy tubes and conservative testing. Anemia can be treated with erythropoiesis-stimulating agents, as well as iron, folate, and B12 when indicated. Although there are limited retrospective studies and no prospective studies to guide management, prior reports suggest that outcomes for surgical patients managed without ABTs are comparable to historic controls. A recent risk-adjusted, propensity-matched, case-control study of outcomes of all hospitalized patients who refused ABT at a large academic health center showed that bloodless management was not an independent predictor of adverse outcomes. Surprisingly, there was a lower overall mortality in the bloodless group and discharge hemoglobin levels were similar for both bloodless and control groups. Further research is now needed to optimize therapy and identify novel interventions to manage bloodless patients. Lessons learned from bloodless patients are likely to benefit all patients given recent evidence suggesting that patients who avoid ABTs do as well, if not better, than those who accept transfusions.
Combining Mutual Information and Scale Invariant Feature Transform for Fast and Robust Multisensor SAR Image Registration (2009)

The Scale Invariant Feature Transform (SIFT) operator&amp;apos;s success for computer vision applications makes it an attractive solution for the intricate feature based SAR image registration problem. For SAR images, SIFT feature matching results into lot of false alarms. To overcome the mentioned problem, we propose to use mutual information (MI) along with the SIFT operator for SAR image registration and matching applications. MI is an established multimodal registration similarity metric and has the capability to quickly estimate rough registration parameters from down-sampled images. The rough image registration parameters obtained using MI can be introduced for conjugate feature selection during the SIFT matching phase. Introduction of MI to the SIFT processing chain not only reduces the number of false alarms drastically but also helps to increase the number of matches as the operator detection and matching thresholds can be relaxed, relying on the available mutual information estimate. Further, the matching consistency of the SIFT matches especially for SAR images with various acquisition differences might not be up to the desired levels. To tackle the observed phenomenon, MI
Interconnection Formation by Doping Chemical‐Vapor‐Deposition Aluminum with Copper Simultaneously: Al‐Cu CVD (1994)

A novel chemical vapor deposition (CVD) method to form Al‐Cu wiring and via filling by simultaneous doping with Cu has been developed and its use demonstrated for advanced ultralarge scale integration applications. This new Al‐Cu CVD method was realized by using appropriate Al and Cu dimethylaluminumhydride and cyclopentadienylcoppertri‐ethylphosphine as metalorganic precursors. The deposited Al‐Cu film had a highly uniform Cu distribution and contained the phase which is indicative of a hypoeutectic Al‐Cu alloy applicable to practical interconnections. This work also showed that the electrical resistance and electromigration endurance of CVD Al can be improved by Cu incorporation with this simultaneous Cu doping method.
Pigment Epithelium-Derived Factor (PEDF) Binds to Glycosaminoglycans:  Analysis of the Binding Site (1998)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionNEXTORIGINAL ARTICLEThis notice is a correctionPigment Epithelium-Derived Factor (PEDF) Binds to Glycosaminoglycans: Analysis of the Binding SiteElena Alberdi, C. Craig Hyde, and Cite this: Biochemistry 1998, 37, 51, 18128Publication Date (Web):November 26, 1998Publication History Published online26 November 1998Published inissue 1 December 1998https://pubs.acs.org/doi/10.1021/bi985058thttps://doi.org/10.1021/bi985058tcorrectionACS PublicationsCopyright © Not subject to U.S. Copyright. Published 1998 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 Views216Altmetric-Citations-LEARN 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 (20 KB) Get e-Alertsclose Get e-Alerts
Enzymic resynthesis of the hydrolyzed peptide bond(s) in ribonuclease S (1979)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEnzymic resynthesis of the hydrolyzed peptide bond(s) in ribonuclease SGene A. Homandberg and Michael LaskowskiCite this: Biochemistry 1979, 18, 4, 586–592Publication Date (Print):February 20, 1979Publication History Published online1 May 2002Published inissue 20 February 1979https://pubs.acs.org/doi/10.1021/bi00571a006https://doi.org/10.1021/bi00571a006research-articleACS PublicationsRequest reuse permissionsArticle Views99Altmetric-Citations71LEARN 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 transcriptomic and proteomic analysis of the effect of CpG‐ODN on human THP‐1 monocytic leukemia cells (2005)

The CpG motif of bacterial DNA (CpG-DNA) is a potent immunostimulating agent whose mechanism of action is not yet clear. Here, we used both DNA microarray and proteomic approaches to investigate the effects of oligodeoxynucleotides containing the CpG motif (CpG-ODN) on gene transcription and protein expression profiles of CpG-ODN responsive THP-1 cells. Microarray analysis revealed that 2 h stimulation with CpG-ODN up-regulated 50 genes and down-regulated five genes. These genes were identified as being associated with inflammation, antimicrobial defense, transcriptional regulation, signal transduction, tumor progression, cell differentiation, proteolysis and metabolism. Longer stimulation (8 h) with CpG-ODN enhanced transcriptional expression of 58 genes. Among these 58 genes, none except one, namely WNTI inducible signaling pathway protein 2, was the same as those induced after 2 h stimulation. Proteomic analysis by two-dimensional gel electrophoresis, followed by mass spectrometry identified several proteins up-regulated by CpG-ODN. These proteins included heat shock proteins, modulators of inflammation, metabolic proteins and energy pathway proteins. Comparison of microarray and proteomic expression profiles showed poor correlation. Use of more reliable and sensitive analyses, such as reverse transcriptase polymerase chain reaction, Western blotting and functional assays, on several genes and proteins, nonetheless, confirmed that there is indeed good correlation between mRNA and protein expression after CpG-ODN treatment. This study also revealed that several anti-apoptotic and neuroprotective related proteins, not previously reported, are activated by CpG-DNA. These findings have extended our knowledge on the activation of cells by CpG-DNA and may contribute to further understanding of mechanisms that link innate immunity with acquired immune response(s).
Heterogeneity of the first cluster of differentiation: characterization and epitopic mapping of three CD1 molecules on normal human thymus cells. (1986)

In humans, the presence of two non-HLA class 1-like molecules, whose expression, similar to murine Tla, is restricted to cortical thymocytes, has been shown with monoclonal antibodies defining the first cluster of differentiation (CD1). We report here with the use of 12 anti-CD1 antibodies and a combination of technical approaches, the characterization of a third CD1 molecule. We show that we can presently define seven different epitopes on the three CD1 molecules: four epitopes are restricted to the 49,000 dalton molecule, two epitopes to the 45,000 dalton molecule, and one epitope to the 43,000 dalton molecule. We show that the association of the newly identified 45,000 dalton heavy chain with human beta2-microglobulin is weak. In addition we show the presence of a fourth non-HLA class I molecular species on the surface of normal human thymus cells.
Effects of the configuration of a multi-epitope chimeric malaria DNA vaccine on its antigenicity to mice. (1999)

This study demonstrated that both combination and configuration of the epitope may affect the antigenicity of a chimeric multiple antigen.
Prostate-Specific–Antigen Testing for Early Diagnosis of Prostate Cancer (2001)

This Journal feature begins with a case vignette highlighting a common clinical problem. Evidence supporting various strategies is then presented, followed by a review of formal guidelines, when they exist. The article ends with the author's clinical recommendations.A 65-year-old man with no risk factors for prostate cancer except his age has a normal digital rectal examination. Should a prostate-specific–antigen (PSA) test be ordered?The Clinical ProblemThe introduction of PSA testing in 1987 resulted in an enormous increase in the reported incidence of prostate cancer in the United States. After peaking in 1992, the incidence fell, presumably owing to the identification of preexisting cases among men who had been tested. The rate of death from prostate cancer has risen and fallen over the same period for reasons that are unclear (Figure 1).1 Advocates of screening attribute . . .
A cDNA cloning vector that permits expression of cDNA inserts in mammalian cells. (1983)

This paper describes a plasmid vector for cloning cDNAs in Escherichia coli; the same vector also promotes expression of the cDNA segment in mammalian cells. Simian virus 40 (SV40)-derived DNA segments are arrayed in the pcD vector to permit transcription, splicing, and polyadenylation of the cloned cDNA segment. A DNA fragment containing both the SV40 early region promoter and two introns normally used to splice the virus 16S and 19S late mRNAs is placed upstream of the cDNA cloning site to ensure transcription and splicing of the cDNA transcripts. An SV40 late region polyadenylation sequence occurs downstream of the cDNA cloning site, so that the cDNA transcript acquires a polyadenylated 3' end. By using pcD-alpha-globin cDNA as a model, we confirmed that the alpha-globin transcript produced in transfected cells is initiated correctly, spliced at either of the two introns, and polyadenylated either at the site coded in the cDNA segment or at the distal SV40 polyadenylation signal. A cDNA clone library constructed with mRNA from SV40-transformed human fibroblasts and this vector (about 1.4 X 10(6) clones) yielded full-length cDNA clones that express hypoxanthine-guanine phosphoribosyltransferase (Jolly et al., Proc. Natl. Acad. Sci. U.S.A., in press).
Natural autoantibodies reactive with glycosaminoglycans in rheumatoid arthritis (2008)

The highly abundant and cross-reactive, GAG-specific natural autoantibodies in serum may serve as novel disease-state markers in patients with rheumatoid arthritis.
Automatic evaluation of Dutch pronunciation by using speech recognition technology (2002)

The ultimate aim of the research reported on in this paper is to develop a system for automatic assessment of foreign speakers' pronunciation of Dutch. The aim of the experiment was to determine whether pronunciation ratings assigned by human experts could be predicted on the basis of scores calculated by an automatic speech recognizer. To this end 20 native and 60 non-native speakers of Dutch read ten phonetically rich sentences over the telephone. The automatic speech recognizer was trained with read speech of 4019 Dutch subjects with varying regional accents. The results show that the human scores can be accurately predicted, even in the case of telephone speech. Analysis of the various types of human ratings and automatic measures provides more insight into the relationship between human and machine scores and indicates how the automatic measures can be further improved to achieve even greater predictive power.
Automated segmentation of the macula by optical coherence tomography (2009)

This paper presents optical coherence tomography (OCT) signal intensity variation based segmentation algorithms for retinal layer identification. Its main ambition is to reduce the calculation time required by layer identification algorithms. Two algorithms, one for the identification of the internal limiting membrane (ILM) and the other for retinal pigment epithelium (RPE) identification are implemented to evaluate structural features of the retina. Using a 830 nm spectral domain OCT device, this paper demonstrates a segmentation method for the study of healthy and diseased eyes.
IMP: Instance Mask Projection for High Accuracy Semantic Segmentation of Things (2019)

In this work, we present a new operator, called Instance Mask Projection (IMP), which projects a predicted Instance Segmentation as a new feature for semantic segmentation. It also supports back propagation so is trainable end-to-end. Our experiments show the effectiveness of IMP on both Clothing Parsing (with complex layering, large deformations, and non-convex objects), and on Street Scene Segmentation (with many overlapping instances and small objects). On the Varied Clothing Parsing dataset (VCP), we show instance mask projection can improve 3 points on mIOU from a state-of-the-art Panoptic FPN segmentation approach. On the ModaNet clothing parsing dataset, we show a dramatic improvement of 20.4% absolutely compared to existing baseline semantic segmentation results. In addition, the instance mask projection operator works well on other (non-clothing) datasets, providing an improvement of 3 points in mIOU on Thing classes of Cityscapes, a self-driving dataset, on top of a state-of-the-art approach.
Studies on the mechanism of action of an antibody-targetted drug-carrier conjugate. (1985)

A conjugate of methotrexate-substituted human serum albumin (HSA) coupled to a monoclonal antibody (791T/36) recognizing osteogenic sarcoma cell lines has been reported previously to have good cytotoxicity and specificity in vitro (Garnett et al., 1983). Cytotoxicity was assessed by the median inhibition (IC50) of [75Se]selenomethionine uptake resulting from a 24-h incubation of conjugate with antigen-bearing 788T or 791T osteogenic sarcoma cell lines. In the present work, the properties of this conjugate have been investigated to determine whether cytotoxicity is optimal with respect to binding activity, and aspects of the mechanism of action investigated by the effects of specific inhibitors of biochemical processes on conjugate cytotoxicity. Conjugate cytotoxicity was reduced by ammonium chloride suggesting that endocytosis and an acidic internal compartment were involved in the mechanism of action. The specific inhibitors of proteinases leupeptin and E64 also reduced conjugate cytotoxicity, while the inhibitors pepstatin A and chymostatin had no effect, demonstrating that cysteine proteinases were involved. The inhibitor of methotrexate transport, folinic acid, reduced the cytotoxicity of conjugate more than that of free methotrexate whereas folic acid had no effect on either, indicating that the methotrexate transport system may still be involved but in a different manner to the free drug. The cytotoxicity of these conjugates is probably near optimal for maximum selectivity.
Special Feature: GaN for Opto- and Power-electronic Applications (2) Characterization of GaN-related materials using high-resolution XRD (2014)

Although high-resolution X-ray diffraction (HR-XRD) has been commonly employed for the crystallinity characterization of GaN-related materials, special care is required due to the complexities resulting from peculiar features in GaN-related materials, as explained in the preceding article. General explanation for the application of HR-XRD techniques to the characterization of semiconductor epitaxial films or bulk single crystals can be found in various textbooks (1) –(5) . Therefore, this article will focus on special considerations to be taken in the application of the HR-XRD technique to GaN and related optoelectronic and power-electronic device materials. In addition, the latest hot topics in the HR-XRD characterization techniques for GaN-related materials will be shortly reviewed. 2. Crystallographic features of GaN
Syndecan-2 Exerts Antifibrotic Effects by Promoting Caveolin-1–mediated Transforming Growth Factor-β Receptor I Internalization and Inhibiting Transforming Growth Factor-β1 Signaling (2013)

Alveolar macrophage syndecan-2 exerts antifibrotic effects by promoting caveolin-1-dependent TGF-β1 and TβRI internalization and inhibiting TGF-β1 signaling in alveolar epithelial cells. Hence, molecules that facilitate TβRI degradation via endocytosis represent potential therapies for pulmonary fibrosis.
Unilateral Versus Bilateral Sacral Neuromodulation in Patients With Chronic Voiding Dysfunction (2002)

Bilateral is in general not superior to unilateral sacral neuromodulation. However, in some individuals bilateral stimulation may be more effective in relieving symptoms. Therefore, if unilateral percutaneous nerve evaluation fails, a bilateral test should be considered.
Site2 binding energetics of the regulatory step of growth hormone–induced receptor homodimerization (2003)

Receptor signaling in the growth hormone (GH)-growth hormone receptor (GHR) system is controlled through a sequential two-step hormone-induced dimerization of two copies of the extracellular domain (ECD) of the receptor. The regulatory step of this process is the binding of the second ECD (ECD2) to the stable preassociated 1 : 1 GH/ECD1 complex on the cell surface. To determine the energetics that governs this step, the binding kinetics of 38 single- and double-alanine mutants in the hGH Site2 contact with ECD2 were measured by using trimolecular surface plasmon resonance (TM-SPR). We find that the Site2 interface of hGH does not have a distinct binding hot-spot region, and the most important residues are not spatially clustered, but rather are distributed over the whole binding surface. In addition, it was determined through analysis of a set of pairwise double alanine mutations that there is a significant degree of negative cooperativity among Site2 residues. Residues that show little effect or even improved binding on substitution with alanine, when paired with D116A-hGH, display significant negative cooperativity. Because most of these pairwise mutated residues are spatially separated by >or=10 A, this indicates that the Site2 binding interface of the hGH-hGHR ternary complex displays both structural and energetic malleability.
Inhibition of HIV Budding by a Genetically Selected Cyclic Peptide Targeting the Gag−TSG101 Interaction (2008)

The egress of HIV particles from virus-infected cells is accomplished by the recruitment of proteins that normally mediate host cell endocytic functions. This process requires interaction of the HIV Gag protein with the host protein TSG101 (tumor susceptibility gene 101). Here, we report the use of a bacterial reverse two-hybrid system to identify cyclic peptides that interfere with the Gag-TSG101 interaction and the finding that a five amino acid peptide discovered by this approach can disrupt the interaction and consequently inhibit HIV egress. The inhibiting molecule, which was selected from a cyclic peptide library containing approximately 3.2 x 10(6) members, differs in primary sequence from the interacting sites of either TSG101 or Gag. Addition of cyclic peptide tagged with an HIV Tat sequence, which previously has been shown to enhance protein translocation across plasma membranes, to cultured human cells inhibited the production of virus-like particles (VLPs) by these cells (IC(50) of 7 microM), and this inhibition occurred in the absence of adverse affects on normal endocytic functions mediated by TSG101. A mutant Gag protein not dependent on TSG101 for release was unaffected by the cyclic peptide. Our findings, which suggest that interference with the TSG101-Gag interaction by cyclic peptides may be of practical use in the treatment of HIV infections, identify a specific cyclic peptide that reduces VLP release by this mechanism; they also demonstrate that the efficiency of interference with protein-protein interactions by cyclic peptides can be enhanced by tagging the peptides with translocation-promoting sequences. Collectively our results support the notion that small molecule therapeutics that inhibit specific interactions between viral and host proteins may have general applicability in antiviral therapy.
Recent advances in pre-clinical mouse models of COPD (2013)

COPD (chronic obstructive pulmonary disease) is a major incurable global health burden and will become the third largest cause of death in the world by 2020. It is currently believed that an exaggerated inflammatory response to inhaled irritants, in particular cigarette smoke, causes progressive airflow limitation. This inflammation, where macrophages, neutrophils and T-cells are prominent, leads to oxidative stress, emphysema, small airways fibrosis and mucus hypersecretion. The mechanisms and mediators that drive the induction and progression of chronic inflammation, emphysema and altered lung function are poorly understood. Current treatments have limited efficacy in inhibiting chronic inflammation, do not reverse the pathology of disease and fail to modify the factors that initiate and drive the long-term progression of disease. Therefore there is a clear need for new therapies that can prevent the induction and progression of COPD. Animal modelling systems that accurately reflect disease pathophysiology continue to be essential to the development of new therapies. The present review highlights some of the mouse models used to define the cellular, molecular and pathological consequences of cigarette smoke exposure and whether they can be used to predict the efficacy of new therapeutics for COPD.