gebhart/patrepeval huggingface dataset:
Absolute Quantitative Detection of Abl Tyrosine Kinase Domain Mutations Using a Novel Microfluidic Platform and Allele-Specific PCR. (2005)

Abstract Point mutations in the Abl tyrosine kinase domain are the main mechanism of secondary resistance to imatinib mesylate (IM) therapy in chronic myeloid leukemia (CML) patients. Current mutation detection approaches including direct sequencing, DHPLC, and SSCP range in sensitivity from 5% to 20%. Detection of mutations in early treatment and possibly pre-treatment samples could allow patient therapy to be altered before resistance is detected cytogenetically or disease progression. A sensitive assay using a novel nanofluidic chip designed for digital isolation and detection (DID) by mutant allele-specific amplification was used to detect rare mutant copies of Abl in a very high background of wild-type (Wt) Abl cDNA. The DID chip partitions a nucleic acid sample into thousands of isolated reaction chambers, thereby enriching rare targets and enabling absolute quantitative, specific and sensitive detection of rare sequences and mutations. Each sample mix of 7.2 mcl containing the necessary reagents for a quantitative PCR 5′-nuclease assay is filled into a nanofluidic network. The sample is partitioned into 1,200 chambers using microfluidic valves fabricated by multilayer-soft-lithography. Each 6 nl reaction chamber contains a fraction of the original nucleic acid sample and reagents for detecting the target of interest. Since the mutant target is rare, the majority of partitions will not contain the mutant, while a small number of partitions will contain just one mutant copy. Single copy detection using the DID chip is reproducible and reliable. For initial proof of concept experiments a set of assays able to detect a group of p-loop mutations and the T315I mutation were optimized using model mixtures. Studies by French centers and Australian groups suggest that these mutations confer worse prognosis and the T315I mutation is refractory to other targeted therapies. Mutation-specific PCR assays were developed for the following mutations: G250E, Q252H (2 substitutions), Y253F, E255K, E255V, and T315I. Initial experiments utilized mutated Bcr-Abl cDNA and plasmids serially diluted into the background of 105 equivalents of Wt Bcr-Abl cDNA from a transformed BaF3 cell line. As few as 9-88 copies were specifically and reliably detected in each of the mutation-specific assays in the background of 105 Wt copies. A non-extendable blocker primer for the Wt and streptavidin beads are also being tested to enrich for mutants prior to PCR. Wt Abl is also quantified to allow for the determination of percent Abl mutated in the assays applied to clinical samples. Conclusion: This method utilizes a novel platform to provide highly sensitive and specific detection of known point mutations and can be applied to early clinical samples. The assay is unique in that it can be extended to a large group of mutations as detection is achieved in very small amounts of rare samples partitioned into thousands of wells prior to PCR. Figure 1 Figure 1.
The immunosuppressant FTY720 is phosphorylated by sphingosine kinase type 2 (2003)

The potent immunosuppressive drug FTY720, a sphingosine analog, induces redistribution of lymphocytes from circulation to secondary lymphoid tissues. FTY720 is phosphorylated in vivo and functions as an agonist for four G-protein-coupled sphingosine-1-phosphate receptors. The identity of the kinase that phosphorylates FTY720 is still not known. Here we report that although both sphingosine kinase type 1 (SphK1) and type 2 (SphK2) can phosphorylate FTY720 with low efficiency, SphK2 is much more effective than SphK1. FTY720 inhibited phosphorylation of sphingosine catalyzed by SphK2 to a greater extent than it inhibits SphK1. Thus, SphK2 may be the relevant enzyme that is responsible for in vivo phosphorylation of FTY720.
Size- and shape-dependent peroxidase-like catalytic activity of MnFe2O4 Nanoparticles and their applications in highly efficient colorimetric detection of target cancer cells (2015)

The catalytic activity of nanocrystal catalysts depends strongly on their chemical composition, size, and shape. Herein, we report four different sizes and shapes of MnFe2O4 nanoparticles (NPs) prepared by a hydrothermal procedure. In addition, the size- and shape-dependent peroxidase-like activity of these NPs was first explored using 3,3',5,5'-tetramethyl-benzidine and H2O2 as peroxidase substrates. The results showed that the peroxidase-like activities of the MnFe2O4 NPs were size- and shape-dependent and followed the order of 4 nm (spherical) > 18 nm (plate-like) > 27 nm (near-cubic) > 16 nm (spherical); this order was closely related to their surface-to-volume ratio and atom arrangements. Such an investigation is of great significance for peroxidase nanomimetics with enhanced activity and utilization. Furthermore, folic acid (FA)-conjugated MnFe2O4 NPs allow the detection of folate receptor-rich cancer cells. Such investigation can be widely utilized for the identification of important target molecules.
Fish oil supplementation & coronary artery disease: does it help? (2012)

Omega-3 polyunsaturated fatty acids (PUFAs) have been shown to decrease the risk of cardiovascular disease. They reduce fatal and non-fatal myocardial infarction, stroke, coronary artery disease (CAD), sudden cardiac death, and all-cause mortality. They are well tolerated and cause minimal adverse effects. In this review, we sought to provide an overview of the current literature on the use of Omega-3 fatty acids for the treatment of CAD and discuss the possible benefits.
Cytokines: An Overview (1991)

Cytokines are a broad, heterogeneous group of proteins and polypeptides that regulate intercellular communication. Examples of cytokines include interleukins, interferons, colony-stimulating factors, and a variety of growth factors. The preparation of large quantities of highly purified recombinant cytokines has provided a basis for their biological and physicochemical characterization. The pleiotropic biological effects of these factors are expressed through binding to specific, high-affinity cell-surface receptors. Although they are different in amino acid sequence, cytokines have a number of biological and physicochemical properties in common.
Quantification of Regulatory T Cells Enables the Identification of High-Risk Breast Cancer Patients and Those at Risk of Late Relapse (2006)

These findings indicate that quantification of FOXP3-positive TR in breast tumors is valuable for assessing disease prognosis and progression, and that TR are an important therapeutic target for breast cancer. FOXP3-positive TR represent a novel marker for identifying late-relapse patients who may benefit from aromatase therapy after standard tamoxifen treatment.
High serum coenzyme Q10, positively correlated with age, selenium and cholesterol, in Inuit of Greenland. A pilot study (1999)

Greenlanders (Eskimos) have low prevalence of ischaemic heart disease, partly explained by a lower extent of atherosclerosis and a low n-6/n-3 ratio of polyunsaturated fatty acids. As atherosclerosis is also a result of oxidative stress, the total antioxidative readiness could have a substantial impact. From a health survey we chose the subpopulation from the most remote area, where the traditional Greenlandic diet with high intake of sea mammals and fish predominates. The mean (SD) of S-CoQ10 in males was 1.495 (0.529) nmol/ml and 1.421 (0.629) nmol/ml in females, significantly higher (p < 0.001) compared to a Danish population. In a linear multiple regression model the S-CoQ10 level is significantly positively associated with age and S-selenium in males, and S-total cholesterol in females. The high level of CoQ10 in Greenlanders probably reflects diet, since no bioaccumulation takes place, and it could probably be a substantial part of the antioxidative defense.
Quality Components of Sea Buckthorn (Hippophaë rhamnoides) Varieties (2005)

The sensory quality and chemical constituents of juices from seven sea buckthorn (Hippophaerhamnoides L.) varieties were studied in two consecutive seasons. The juices were generally described as sour and astringent, with low sweetness and fruity flavor. The differences in sensory quality as well as in chemical composition between samples and years were significant (p < 0.05) in most parameters studied. The Chuiskaya variety was described as the sweetest, with the strongest fruity flavor, whereas the varieties Avgustinka, Botanicheskaya, Trofimovskaya, and Raisa were the sourest and most astringent. Total sugar (fructose and glucose) varied from 1.9 to 7.1 g/100 mL in juice, total acid (malic and quinic acids) from 3.1 to 5.1 g/100 mL, vitamin C from 29 to 176 mg/100 mL, and pulp oil from 0.7 to 3.6%. The soluble solids were between 7.4 and 12.6, the pH between 2.7 and 2.9, and the titrable acidity between 2.0 and 3.7. The redness was highest on Avgustinka and Raisa, but there were no differences in yellowness. Total sugar and the sugar/acid ratio correlated positively with sweetness and negatively with sourness and astringency, whereas total acid and titrable acidity correlated positively with sourness and astringency and negatively with sweetness.
A fluorescent assay for complement activation. (1981)

We report here a rapid assay for the complement enzymes CVFBb, C4b2a and Cls. This assay involves the use of a peptide substrate that releases a fluorescent coumarin derivative (AMC) upon cleavage by the convertase. The substrate, BocLeuGlyArgAMC, was chosen because its sequence is similar to the carboxyl terminus of C3a, and identical to that of C5a. The Km of this substrate are about 125 microM for the C3/5 convertase CVFBb, 169 microM for C4b2a, and 140 microM for C1s.
Antibody Microarray Profiling Reveals Individual and Combined Serum Proteins Associated with Pancreatic Cancer (2005)

We used antibody microarrays to probe the associations of multiple serum proteins with pancreatic cancer and to explore the use of combined measurements for sample classification. Serum samples from pancreatic cancer patients (n = 61), patients with benign pancreatic disease (n = 31), and healthy control subjects (n = 50) were probed in replicate experiment sets by two-color, rolling circle amplification on microarrays containing 92 antibodies and control proteins. The antibodies that had reproducibly different binding levels between the patient classes revealed different types of alterations, reflecting inflammation (high C-reactive protein, alpha-1-antitrypsin, and serum amyloid A), immune response (high IgA), leakage of cell breakdown products (low plasma gelsolin), and possibly altered vitamin K usage or glucose regulation (high protein-induced vitamin K antagonist-II). The accuracy of the most significant antibody microarray measurements was confirmed through immunoblot and antigen dilution experiments. A logistic-regression algorithm distinguished the cancer samples from the healthy control samples with a 90% and 93% sensitivity and a 90% and 94% specificity in duplicate experiment sets. The cancer samples were distinguished from the benign disease samples with a 95% and 92% sensitivity and an 88% and 74% specificity in duplicate experiment sets. The classification accuracies were significantly improved over those achieved using individual antibodies. This study furthered the development of antibody microarrays for molecular profiling, provided insights into the nature of serum-protein alterations in pancreatic cancer patients, and showed the potential of combined measurements to improve sample classification accuracy.
Surface Modification for Improved Blood Compatibility (1988)

Several surface modification techniques are currently being used to improve the biocompatibility of blood-contacting devices. These include the immobilization of bioactive materials to prevent thrombus generation and platelet activation, the incorporation of hydrophilic grafts onto practical hydrophobic surfaces (polyurethanes) to reduce protein adsorption, and the concept of microdomain-phase separated surfaces to regulate cellular and protein adhesion.
Reaction of ethynyl compounds with lactones (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReaction of ethynyl compounds with lactonesHaruo Ogura, Hiroshi Takahashi, and Tsuneo ItohCite this: J. Org. Chem. 1972, 37, 1, 72–75Publication Date (Print):January 1, 1972Publication History Published online1 May 2002Published inissue 1 January 1972https://pubs.acs.org/doi/10.1021/jo00966a020https://doi.org/10.1021/jo00966a020research-articleACS PublicationsRequest reuse permissionsArticle Views336Altmetric-Citations39LEARN 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
Genetic Engineering of Escherichia coli for Biofuel Production (2010)

In order to mitigate climate change without adversely affecting global energy supply, there is growing interest in the possibility of producing transportation fuels from renewable sources via microbial fermentation. Central to this challenge is the design of biocatalysts that can efficiently convert cheap lignocellulosic raw materials into liquid fuels. Owing to the wealth of genetic and metabolic knowledge associated with Escherichia coli, this bacterium is the most convenient starting point for engineering microbial catalysts for biofuel production. Here, we review the range of liquid fuels that can be produced in E. coli and discuss the underlying biochemistry that enables these metabolic products. The fundamental and technological challenges encountered in the development of efficient fermentation processes for biofuel production are highlighted. The example of biodiesel is a particularly illustrative case study and is therefore discussed in detail.
Advances in Surgical Treatment of Atrial Fibrillation (2007)

Atrial fibrillation (AF) is the most common sustained arrhythmia. It is associated with increased risks of death and stroke; most strokes in AF patients are thought to arise from thrombi in the left atrial appendage. Surgical ablation of AF includes excision of the left atrial appendage and is an effective means of treating this arrhythmia, with the classic Maze procedure curing AF in >90% of patients and virtually eliminating the risk of late stroke. A complex but safe operation, the Maze procedure has been applied by relatively few surgeons. However, recent advances in the understanding of the pathogenesis of AF and development of new ablation technologies enable surgeons to perform pulmonary vein ablation, create linear left atrial lesions, and remove the left atrial appendage rapidly and safely. Lesions are created under direct vision, minimizing the risk of damage to the pulmonary veins and adjacent mediastinal structures. The majority of surgical ablation procedures have been performed in conjunction with mitral valve surgery, with the combination of mitral valve repair and cure of AF enabling patients to avoid lifelong anticoagulation. Recently developed surgical instrumentation now enables thoracoscopic and keyhole approaches, facilitating extension of epicardial AF ablation and excision of the left atrial appendage to patients with isolated AF and no other indication for cardiac surgery. In addition, novel devices designed specifically for minimally invasive epicardial exclusion of the left atrial appendage will broaden the range of treatment options for patients with AF, possibly eliminating the need for anticoagulation in selected patients.
Multimode optical imaging for translational chemotherapy: in vivo tumor detection and delineation by targeted gallium corroles (2011)

We report the feasibility of tumor detection and delineation <i>in vivo</i> using multimode optical imaging of targeted gallium corrole (HerGa). HerGa is highly effective for targeted HER2+ tumor elimination <i>in vivo</i>, and it emits intense fluorescence. These unique characteristics of HerGa prompted us to investigate the potential of HerGa for tumor detection and delineation, by performing multimode optical imaging <i>ex vivo</i> and <i>in vivo</i>; the imaging modes included fluorescence intensity, spectral (including ratiometric), lifetime, and two-photon excited fluorescence, using our custom-built imaging system. While fluorescence intensity imaging provided information about tumor targeting capacity and tumor retention of HerGa, ratiometric spectral imaging offered more quantitative and specific information about HerGa location and accumulation. Most importantly, the fluorescence lifetime imaging of HerGa allowed us to discriminate between tumor and non-tumor regions by fluorescence lifetime differences. Finally, two-photon excited fluorescence images provided highly resolved and thus topologically detailed information around the tumor regions where HerGa accumulates. Taken together, the results shown in this report suggest the feasibility of tumor detection and delineation by multimode optical imaging of HerGa, and fluorescent chemotherapy agents in general. Specifically, the multimode optical imaging can offer complementary and even synergetic information simultaneously in the tumor detection and delineation by HerGa, thus enhancing contrast.
Genetic and Biochemical Dissection of Transgenic RNA-Mediated Virus Resistance (1996)

Joel Goodwin, Kelly Chapman, Sherri Swaney, T. Dawn Parks, Earl A. Wernsman, William G. Dougherty, Genetic and Biochemical Dissection of Transgenic RNA-Mediated Virus Resistance, The Plant Cell, Vol. 8, No. 1 (Jan., 1996), pp. 95-105
NRC's PORTAGE system for WMT 2007 (2007)

We present the PORTAGE statistical machine translation system which participated in the shared task of the ACL 2007 Second Workshop on Statistical Machine Translation. The focus of this description is on improvements which were incorporated into the system over the last year. These include adapted language models, phrase table pruning, an IBM1-based decoder feature, and rescoring with posterior probabilities.
Identification of Multiple ς 54 -Dependent Transcriptional Activators in Vibrio cholerae (1998)

In the pathogenic bacterium Vibrio cholerae, the alternate sigma factor sigma54 is required for expression of multiple sets of genes, including an unidentified gene(s) necessary for enhanced colonization within the host. To identify sigma54-dependent transcriptional activators involved in colonization, PCR was performed with V. cholerae chromosomal DNA and degenerate primers, revealing six novel and distinct coding sequences with homology to sigma54-dependent activators. One sequence had high homology to the luxO gene of V. harveyi, which in that organism is involved in quorum sensing. Phenotypes of V. cholerae strains containing mutations in each of the six putative sigma54-dependent activator genes identified one as a probable ntrC homologue. None of the mutant strains exhibited a defect in the ability to colonize infant mice, suggesting the presence of additional sigma54-dependent activators not identified by this technique.
Role of the lncRNA-p53 regulatory network in cancer (2014)

Advances in functional genomics have led to discovery of a large group of previous uncharacterized long non-coding RNAs (lncRNAs). Emerging evidence indicates that lncRNAs may serve as master gene regulators through various mechanisms. Dysregulation of lncRNAs is often associated with a variety of human diseases including cancer. Of significant interest, recent studies suggest that lncRNAs participate in the p53 tumor suppressor regulatory network. In this review, we discuss how lncRNAs serve as p53 regulators or p53 effectors. Further characterization of these p53-associated lncRNAs in cancer will provide a better understanding of lncRNA-mediated gene regulation in the p53 pathway. As a result, lncRNAs may prove to be valuable biomarkers for cancer diagnosis or potential targets for cancer therapy.
Prognostic nomogram and index for overall survival in previously untreated patients with chronic lymphocytic leukemia (2007)

The clinical course for patients with chronic lymphocytic leukemia is extremely heterogeneous. The Rai and Binet staging systems have been used to risk-stratify patients; most patients present with early-stage disease. We evaluated a group of previously untreated patients with chronic lymphocytic leukemia (CLL) at initial presentation to University of Texas M. D. Anderson Cancer Center to identify independent characteristics that predict for overall survival. Clinical and routine laboratory characteristics for 1674 previously untreated patients who presented for evaluation of CLL from 1981 to 2004 were included. Univariate and multivariate analyses identified several patient characteristics at presentation that predicted for overall survival in previously untreated patients with CLL. A multivariate Cox proportional hazards model was developed, including the following independent characteristics: age, beta-2 microglobulin, absolute lymphocyte count, sex, Rai stage, and number of involved lymph node groups. Inclusion of patients from a single institution and the proportion of patients younger than 65 years may limit this model. A weighted prognostic model, or nomogram, predictive for overall survival was constructed using these 6 characteristics for 5- and 10-year survival probability and estimated median survival time. This prognostic model may help patients and clinicians in clinical decision making as well as in clinical research and clinical trial design.
Executive Introduction to Directory Services Using the X.500 Protocol (1992)

This document is an Executive Introduction to Directory Services using the X.500 protocol. It briefly discusses the deficiencies in currently deployed Internet Directory Services, and then illustrates the solutions provided by X.500. This FYI RFC is a product of the Directory Information Services (pilot) Infrastructure Working Group (DISI). A combined effort of the User Services and the OSI Integration Areas of the Internet Engineering Task Force (IETF).