gebhart/patrepeval huggingface dataset:
Intravenous injection of apoptotic leukocytes enhances bone marrow engraftment across major histocompatibility barriers (2001)

Cross-tolerization of T lymphocytes after apoptotic cell uptake by dendritic cells may be involved in self-tolerance maintenance. Furthermore, immunosuppressive properties are attributed to apoptotic cells. This study evaluated the consequences of apoptotic leukocyte administration in a restrictive engraftment model of murine bone marrow (BM) transplantation. Sublethally irradiated recipients received a limited number of allogeneic BM, with or without irradiated apoptotic leukocytes of different origins. No graft-versus-host disease was observed. Whereas only a low proportion of mice receiving BM cells alone engrafted, addition of apoptotic irradiated leukocytes, independently of the origin (donor, recipient, third-party mice, as well as xenogeneic peripheral blood mononuclear cells), significantly enhanced engraftment. Similar results were obtained after infusion of leukocytes rendered apoptotic by UVB irradiation or by anti-Fas monoclonal antibody stimulation, thus confirming the role of apoptotic cells in engraftment facilitation. Overall, these results suggest that apoptotic leukocytes can nonspecifically facilitate allogeneic BM engraftment. Such a simple approach could be of interest in BM transplantation settings involving an important HLA donor/recipient disparity, a T-cell-depleted graft, or reduced conditioning regimen intensity.
Identification of ARA70 as a Ligand-enhanced Coactivator for the Peroxisome Proliferator-activated Receptor γ (1999)

In an effort to understand transcriptional regulation by the peroxisome proliferator-activated receptor gamma (PPARgamma), we have investigated its potential interaction with coregulators and have identified ARA70 as a ligand-enhanced coactivator. ARA70 was initially described as a coactivator for the androgen receptor (AR) and is expressed in a range of tissues including adipose tissue (Yeh, S., and Chang, C. (1996) Proc. Natl. Acad. Sci. U. S. A. 93, 5517-5521). Here we show that ARA70 and PPARgamma specifically interact by coimmunoprecipitation and in a mammalian two-hybrid assay. PPARgamma and ARA70 interact in the absence of the PPARgamma ligand 15-deoxy-Delta12,14-prostaglandin J2, although the addition of exogenous ligand enhances this interaction. Similarly, in transient transfection of DU145 cells, cotransfection of PPARgamma and ARA70 induces transcription from reporter constructs driven by either three copies of an isolated PPAR response element or the natural promoter of the adipocyte fatty acid-binding protein 2 in the absence of exogenous 15-deoxy-Delta12,14-prostaglandin J2. However, this PPARgamma-ARA70 transactivation is enhanced by the addition of ligand. Thus, ARA70 can function as a ligand-enhanced coactivator of PPARgamma. Finally, we show that AR can squelch PPARgamma-ARA70 transactivation, which suggests that cross-talk may occur between PPARgamma- and AR-mediated responses in adipocytes.
Migraine — Current Understanding and Treatment (2002)

Migraine is a common and sometimes debilitating disorder. This review describes the epidemiology, pathophysiology, and preventive and symptomatic treatment of migraine, with special attention to drug therapy with the triptans.
Bayesian statistical analysis of protein side‐chain rotamer preferences (1997)

We present a Bayesian statistical analysis of the conformations of side chains in proteins from the Protein Data Bank. This is an extension of the backbone-dependent rotamer library, and includes rotamer populations and average chi angles for a full range of phi, psi values. The Bayesian analysis used here provides a rigorous statistical method for taking account of varying amounts of data. Bayesian statistics requires the assumption of a prior distribution for parameters over their range of possible values. This prior distribution can be derived from previous data or from pooling some of the present data. The prior distribution is combined with the data to form the posterior distribution, which is a compromise between the prior distribution and the data. For the chi 2, chi 3, and chi 4 rotamer prior distributions, we assume that the probability of each rotamer type is dependent only on the previous chi rotamer in the chain. For the backbone-dependence of the chi 1 rotamers, we derive prior distributions from the product of the phi-dependent and psi-dependent probabilities. Molecular mechanics calculations with the CHARMM22 potential show a strong similarity with the experimental distributions, indicating that proteins attain their lowest energy rotamers with respect to local backbone-side-chain interactions. The new library is suitable for use in homology modeling, protein folding simulations, and the refinement of X-ray and NMR structures.
Prediction of dopant ionization energies in silicon: The importance of strain (2003)

Based on a hydrogenic state and strain changes upon defect charging, we propose a simple, parameter-free model that agrees well with the observed group III and V monovalent-impurity ionization energies in Si, revealing the importance of such strain effects. Changes in lattice strain upon defect charging are obtained via superposition and elasticity theory using atomic relaxations from density functional theory.
Linear array of complementary metal oxide semiconductor double-pass metal micromirrors (1997)

Low-cost linear arrays of deflectable micromirrors using a CMOS-compatible process to define both on-chip circuitry and the mirror structure are presented. The mirrors consist of the CMOS second metal layer deposited In two successive passes in order to establish a thick metal layer for the stiff mirror plate as well as a thin one for the flexible hinges. The mirrors are released by sacrificial aluminum and oxide etch Ing. Supercritical point drying is performed in order to avoid sticking of the mirrors lo the substrate. The mirrors are electrostatically deflected by biasing the address electrodes implanted inlo the substrate underneath the mirror plate. Full angular deflection by ::4.8 deg of a 30 x 40-rn 2 plate is achieved with a driving voltage of 11 V. On-chip circuitry adjacent to each mirror allows one to address the pixels with 5-V data pulses. The reflectance of the aluminum surface for wavelengths between 400 and 700 nm was measured to be 83% to 89<>. The mirror surface was further characterized using Auger spectroscopy, showing that no optically rel evant surface modifications occur during postprocessing. The surface rms roughness measured by atomic force microscopy is on the order of 2 5 nm. ll:
Psoriasiform Eruption Induced by Infliximab (2003)

This is the first report of a clinico-pathologic dissociated pattern of cutaneous reaction showing a histopathologic picture of lichenoid dermatitis resulting from infliximab treatment.
The Prevalence of FOXP3 + Regulatory T-Cells in Peripheral Blood of Patients with NSCLC (2009)

We have studied CD4(+)CD25(high)FOXP3(+) regulatory T-cells (T(regs)) from 51 patients with non-small-cell lung cancer (NSCLC) and 33 healthy donors. Regulatory T-cells were identified by fluorescence-activated cell sorting by using a panel of antibodies and by reverse transcriptase polymerase chain reaction analysis for FOXP3 expression. Functional studies were done to analyze their inhibitory role. Finally, regulatory T-cells were analyzed in malignant pleura effusion (PE) from patients with NSCLC. Patients with NSCLC have increased numbers of CD4(+)CD25(high) FOXP3(+) T(regs) in their peripheral blood and pleura effusion (PE), which express high levels of CTLA-4, GITR. These cells were anergic toward T-cell receptor stimulation and, when cocultured with activated CD4(+)CD25(-) cells, potently suppressed their proliferation and cytokine secretion. Our data suggest that in NSCLC patients, there is an increase of CD4(+)CD25(high)FOXP3(+) regulatory T-cells in the peripheral blood and tumor microenvironment. These T-cells might prevent effective antitumor immune responses, and the increase in frequency of CD4(+)CD25(high)FOXP3(+) Tregs might play a role in the modulation of the immune response against NSCLC and could be important in the design of immunotherapeutic approaches.
SOR: Scalable Orthogonal Regression for Non-Redundant Feature Selection and its Healthcare Applications (2012)

As more clinical information with increasing diversity become available for analysis, a large number of features can be constructed and leveraged for predictive modeling. Feature selection is a classic analytic component that faces new challenges due to the new applications: How to handle a diverse set of high dimensional features? How to select features with high predictive power, but low redundant information? How to design methods that can select globally optimal features with theoretical guarantee? How to incorporate and extend existing knowledge driven approach? In this paper, we present Scalable Orthogonal Regression (SOR), an optimization-based feature selection method with the following novelties: 1) Scalability: SOR achieves nearly linear scale-up with respect to the number of input features and the number of samples; 2) Optimality: SOR is formulated as an alternative convex optimization problem with theoretical convergence and global optimality guarantee; 3) Low-redundancy: thanks to the orthogonality objective, SOR is designed specifically to select less redundant features without sacrificing quality; 4) Extendability: SOR can enhance an existing set of preselected features by adding additional features that complement the existing feature set but still with strong predictive power. We present evaluation results showing that SOR consistently outperforms state of the art feature selection methods in a range of quality metrics on several real world data sets. We demonstrate a case study of a large-scale clinical application for predicting early onset of Heart Failure (HF) using real Electronic Health Records (EHRs) data of over 10K patients for over 7 years. Leveraging SOR, we are able to construct accurate and robust predictive models and derive potential clinical insights.
Enhancing Reactivity for Bioorthogonal Pretargeting by Unmasking Antibody-Conjugated trans-Cyclooctenes (2015)

The bioorthogonal cycloaddition reaction between tetrazine and trans-cyclooctene (TCO) is rapidly growing in use for molecular imaging and cell-based diagnostics. We have surprisingly uncovered that the majority of TCOs conjugated to monoclonal antibodies using standard amine-coupling procedures are nonreactive. We show that antibody-bound TCOs are not inactivated by trans-cis isomerization and that the bulky cycloaddition reaction is not sterically hindered. Instead, TCOs are likely masked by hydrophobic interactions with the antibody. We show that introducing TCO via hydrophilic poly(ethylene glycol) (PEG) linkers can fully preserve reactivity, resulting in >5-fold enhancement in functional density without affecting antibody binding. This is accomplished using a novel dual bioorthogonal approach in which heterobifunctional dibenzylcyclooctyne (DBCO)-PEG-TCO molecules are reacted with azido-antibodies. Improved imaging capabilities are demonstrated for different cancer biomarkers using tetrazine-modified fluorophore and quantum dot probes. We believe that the PEG linkers prevent TCOs from burying within the antibody during conjugation, which could be relevant to other bioorthogonal tags and biomolecules. We expect the improved TCO reactivity obtained using the reported methods will significantly advance bioorthogonal pretargeting applications.
Reduced endocytosis and altered lysosome function in cisplatin-resistant cell lines (2003)

We isolated human KB adenocarcinoma cisplatin-resistant (CP-r) cell lines with multidrug-resistance phenotypes because of reduced accumulation of cisplatin and other cytotoxic compounds such as methotrexate and heavy metals. The uptake of horseradish peroxidase (HRPO) and Texas Red dextran was decreased several-fold in KB-CP-r cells, indicating a general defect in fluid-phase endocytosis. In contrast, although EGF receptors were decreased in amount, the kinetics of EGF uptake, a marker of receptor-mediated endocytosis, was similar in sensitive and resistant cells. However, 40-60% of the (125)I-EGF released into the medium after uptake into lysosomes of KB-CP-r cells was TCA precipitable as compared to only 10% released by sensitive cells. These results indicate inefficient degradation of internalised (125)I-EGF in the lysosomes of KB-CP-r cells, consistent with slower processing of cathepsin L, a lysosomal cysteine protease. Treatment of KB cells by bafilomycin A(1), a known inhibitor of the vacuolar proton pump, mimicked the phenotype seen in KB-CP-r cells with reduced uptake of HRPO, (125)I-EGF, (14)C-carboplatin, and release of TCA precipitable (125)I-EGF. KB-CP-r cells also had less acidic lysosomes. KB-CP-r cells were crossresistant to Pseudomonas exotoxin, and Pseudomonas exotoxin-resistant KB cells were crossresistant to cisplatin. Since cells with endosomal acidification defects are known to be resistant to Pseudomonas exotoxin and blocking of endosomal acidification mimics the CP-r phenotype, we conclude that defective endosomal acidification may contribute to acquired cisplatin resistance.
Third-harmonic generation in argon, krypton, and xenon: Bandwidth limitations in the vicinity of Lyman-α (1979)

Using experimentally determined oscillator strengths and photoionization cross-sectional data, we compute the dispersion characteristics of Ar, Kr, and Xe up to their first ionization levels and determine the spectral regions in the VUV where these gases exhibit negative dispersion and so can be efficiently used for frequency tripling. We then investigate the bandwidths over which efficient tripling can be achieved in phase-matched gas mixtures. The bandwidth is limited by the rapidly varying dispersion in the vicinity of resonance transitions in the gases. In particular, we look at the case of frequency tripling 3647 Å radiation to 1215.7 Å (hydrogen Lyman-α) and show, that for fundamental wavelength bandwidths as narrow as 1 Å, the rapid change in refractive index with wavelength can preclude phase matching over the entire bandwidth of the radiation.
TREATMENT OF ACUTE CELLULAR REJECTION WITH T10B9.1A-31 OR OKT3 IN RENAL ALLOGRAFT RECIPIENTS1 (1992)

T10B9.1A-31, a nonmitogenic immunoglobulin Mk monoclonal antibody that detects an epitope on the alpha/beta chains of the T cell antigen receptor (TCR alpha/beta), or OKT3, an anti-CD3 mAb, was employed in a randomized double-blind phase II clinical trial to treat biopsy-proven acute cellular renal allograft rejection. Two of the 40 patients initially selected for the protocol were considered to be nonevaluable. Analysis of the remaining 38 patients receiving both living related and cadaveric donor allografts revealed a patient survival of 100% and a graft survival of 97%. Primary rejection reversal was achieved in 18/19 (95%) patients treated with T10B9.1A-31 and in 20/21 (95%) of patients receiving OKT3. The two patients who did not respond to the first mAb responded to the crossover mAb. Rerejection occurred in 3/18 (17%) of patients treated with T10B9.1A-31 and in 3/20 (15%) treated with OKT3. The mean day of rejection reversal was 1.9 +/- 0.7 with T10B9.1A-31 and 3.37 +/- 1.21 with OKT3 treatment. The rise in mean serum creatinine after mAb administration and the mean creatinine on days 1 through 6 were significantly less in patients treated with T10B9.1A-31. Biopsy specimens analyzed for rejection revealed no significant difference between the T10B9.1A-31 and OKT3 cohorts. The mean serum creatinines at 30, 60, 180, and 360 days posttransplantation were the same for both groups. Significantly fewer febrile, respiratory, and untoward effects followed the first dose (day 0) and fewer febrile, gastrointestinal, and neurological side effects occurred with subsequent doses (days 1-9) in patients treated with T10B9.1A-31. Infectious complications occurred in 3/13 patients treated only with T10B9.1A-31, in 9/17 OKT3-treated patients, and in 4/8 patients treated with both mAb. Analysis of human antimouse antibody (HAMA) revealed that the development of HAMA with T10B9.1A-31 was similar to that of OKT3.
Novel reagent for the fluorometric assay of primary amines (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNovel reagent for the fluorometric assay of primary aminesM. Weigele, S. L. DeBernardo, J. P. Tengi, and W. LeimgruberCite this: J. Am. Chem. Soc. 1972, 94, 16, 5927–5928Publication Date (Print):August 1, 1972Publication History Published online1 May 2002Published inissue 1 August 1972https://pubs.acs.org/doi/10.1021/ja00771a084https://doi.org/10.1021/ja00771a084research-articleACS PublicationsRequest reuse permissionsArticle Views924Altmetric-Citations393LEARN 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
Discovery of a “True” Aspirin Prodrug (2008)

Aspirin prodrugs formed by derivatization at the benzoic acid group are very difficult to obtain because the promoiety accelerates the rate of hydrolysis by plasma esterases at the neighboring acetyl group, generating salicylic acid derivatives. By tracing the hydrolysis pattern of the aspirin prodrug isosorbide-2,5-diaspirinate (ISDA) in human plasma solution, we were able to identify a metabolite, isosorbide-2-aspirinate-5-salicylate, that undergoes almost complete conversion to aspirin by human plasma butyrylcholinesterase, making it the most successful aspirin prodrug discovered to date.
Molecular subtypes and the evolution of treatment management in metastatic colorectal cancer (2020)

Colorectal cancer (CRC) is a heterogeneous disease representing a therapeutic challenge, which is further complicated by the common occurrence of several molecular alterations that confer resistance to standard chemotherapy and targeted agents. Mechanisms of resistance have been identified at multiple levels in the epidermal growth factor receptor (EGFR) pathway, including mutations in <i>KRAS, NRAS</i>, and <i>BRAF</i> <sup>V600E</sup>, and in the HER2 and MET receptors. These alterations represent oncogenic drivers that may co-exist in the same tumor with other primary and acquired alterations <i>via</i> a clonal selection process. Other molecular alterations include DNA damage repair mechanisms and rare kinase fusions, potentially offering a rationale for new therapeutic strategies. In recent years, genomic analysis has been expanded by a more complex study of epigenomic, transcriptomic, and microenvironment features. The Consensus Molecular Subtype (CMS) classification describes four CRC subtypes with distinct biological characteristics that show prognostic and potential predictive value in the clinical setting. Here, we review the panorama of actionable targets in CRC, and the developments in more recent molecular tests, such as liquid biopsy analysis, which are increasingly offering clinicians a means of ensuring optimal tailored treatments for patients with metastatic CRC according to their evolving molecular profile and treatment history.
Needle-probe system for the measurement of tissue refractive index (2007)

Needle-based devices, which are in wide clinical use for needle biopsy procedures, may be augmented by suitable optical techniques for the localization and diagnosis of diseased tissue. Tissue refractive index is one optical contrast mechanism with diagnostic potential. In the case of mammary tissue, for example, recent research indicates that refractive index variations between tissue types may be useful for the identification of cancerous tissue. While many coherence-based forward-sensing devices have been developed to detect scattering changes, none have demonstrated refractive index measurement capabilities. We present a novel needle-based device that is capable of simultaneously measuring refractive index and scattering. Coupled to the sample arm of an optical coherence tomography system, the needle device detects the scattering response and optical pathlength through tissue residing in a fixed-width channel. Near-infrared measurements of tissues and materials with known optical properties using a prototype device will be presented. This work demonstrates the feasibility of integrated in vivo measurement of refractive index and scattering in conjunction with existing clinical needle-based devices.
General considerations for lung function testing (2005)

SERIES “ATS/ERS TASK FORCE: STANDARDISATION OF LUNG FUNCTION TESTING”

Edited by V. Brusasco, R. Crapo and G. Viegi

Number 1 in this Series

⇓In preparing the joint statements on lung function testing for the American Thoracic Society (ATS) and the European Respiratory Society (ERS), it was agreed by the working party that the format of the statements should be modified so that they were easier to use by both technical and clinical staff. This statement contains details about procedures that are common for many methods of lung function testing and, hence, are presented on their own. A list of abbreviations used in all the documents is also included as part of this statement.

All terms and abbreviations used here are based on a report of the American College of Chest Physicians/ATS Joint Committee on Pulmonary Nomenclature 1. The metrology definitions agreed by the International Standards Organization (ISO) are recommended 2 and some important terms are defined as follows.

Accuracy is the closeness of agreement between the result of a measurement and the conventional true value.

Repeatability is the closeness of agreement between the results of successive measurements of the same item carried out, subject to all of the following conditions: same method, same observer, same instrument, same location, same condition of use, and repeated over a short space of time. In previous documents, the term reproducibility was used in this context, and this represents a change towards bringing this document in line with the ISO.

Reproducibility is the closeness of agreement of the results of successive measurements of the same item where the individual measurements are carried out with changed conditions, such as: method of measurement, observer, instrument, location, conditions of use, and time. Thus, if a technician tests a subject several times, this is looking at the …
Cottonseed Oil (2011)

This chapter contains sections titled: Introduction History Seed composition Oil composition Chemical and physical properties of cottonseed oil Processing Cottonseed oil uses Co-product uses References