gebhart/patrepeval huggingface dataset:
Hematological Parameters Improve Prediction of Mortality and Secondary Adverse Events in Coronary Angiography Patients (2015)

Prediction of primary cardiovascular events has been thoroughly investigated since the landmark Framingham risk score was introduced. However, prediction of secondary events after initial events of coronary artery disease (CAD) poses a new challenge. In a cohort of coronary angiography patients (n = 1760), we examined readily available hematological parameters from the UPOD (Utrecht Patient Oriented Database) and their addition to prediction of secondary cardiovascular events. Backward stepwise multivariable Cox regression analysis was used to test their ability to predict death and major adverse cardiovascular events (MACE). Continuous net reclassification improvement (cNRI) and integrated discrimination improvement (IDI) measures were calculated for the hematological parameters on top of traditional risk factors to assess prediction improvement. Panels of 3 to 8 hematological parameters significantly improved prediction of death and adverse events. The IDIs ranged from 0.02 to 0.07 (all P < 0.001) among outcome measures and the cNRIs from 0.11 to 0.40 (P < 0.001 in 5 of 6 outcome measures). In the hematological panels red cell distribution width (RDW) appeared most often. The multivariable adjusted hazard ratio of RDW per 1 standard deviation (SD) increase for MACE was 1.19 [1.08-1.32], P < 0.001. Routinely measured hematological parameters significantly improved prediction of mortality and adverse events in coronary angiography patients. Accurately indicating high-risk patients is of paramount importance in clinical decision-making.
Ordering of water molecules between phospholipid bilayers visualized by coherent anti-Stokes Raman scattering microscopy (2003)

We demonstrate ordered orientation of the hydration water at the surface of phospholipid bilayers by use of coherent anti-Stokes Raman scattering (CARS) microscopy, a highly sensitive vibrational imaging method recently developed. We investigated negatively charged POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-l-serine) and neutral POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) multilamellar onions dispersed in deuterated dodecane. The imaging contrast based on the CARS signal from the H2O stretching vibration shows a clear dependence on the excitation field polarization. Our results provide direct experimental evidence that water molecules close to the phospholipid bilayer surface are ordered with the symmetry axis along the direction normal to the bilayer. Moreover, the amount of ordered water molecules depends on the lipid polar group. The spectral profile for the inter-lamellar water shows that the water molecules bound to the bilayer surface are less hydrogen-bonded and exhibit a higher vibrational frequency than bulk water.
GLUTAMATE-INDUCED NEURONAL NECROSIS IN THE INFANT MOUSE HYPOTHALAMUS (1971)

Journal Article Glutamate-Induced Neuronal Necrosis in the Infant Mouse Hypothalamus: An Electron Microscopic Study Get access John W. Olney, M.D. John W. Olney, M.D. St. Louis, Missouri Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Neuropathology & Experimental Neurology, Volume 30, Issue 1, January 1971, Pages 75–90, https://doi.org/10.1097/00005072-197101000-00008 Published: 01 January 1971
Optimization of confocal epifluorescence microscopy for microchip-based miniaturized total analysis systems (1998)

A confocal epifluorescence detection scheme, optimized to give sub-picomolar detection within planar glass substrates etched to a 30 µm depth, is described. A ×40, 0.6 numerical aperture (N.A.) lens with a 3.7 mm working distance was used to create a focused laser spot about 12 µm in diameter, by under-filling the lens aperture to give an effective, measured N.A. of 0.22 for the laser beam. The sectioning power (optical axis field of view) of various pinholes and the corresponding detector probe volumes (overlap of the excitation and observation volumes) were: (pinhole diameter, sectioning power, probe volume): 100 µm, 18 µm, 0.1 pl; 200 µm, 20 µm, 0.4 pl; 400 µm, 26 µm, 1.7 pl; and 600 µm, 36 µm, 2.4 pl. A log–log plot of fluorescence intensity versus fluorescein concentration, measured in continuous-flow mode using the optimum 400 µm pinhole, showed a correlation coefficient of 0.996 and a slope of 0.85. In this mode, 300 fM fluorescein gave a signal of 34.6 ± 8.1 mV over background with an S/N of 6.1, representing the lowest measured fluorescein dye concentration reported on-chip. Capillary zone electrophoresis of 1 pM fluorescein resulted in a mean S/N of 5.8. The injection plug, estimated to be about 5470 molecules, corresponds to 570 detected molecules on average. The design and use of quick-fit, flangeless fittings for interfacing tubing, fused-silica capillaries or pressurized systems to microfluidic channels etched in planar glass chips is briefly presented.
Biomimetics. Design and Processing of Materials. (1995)

Contents: Biomimetics: Natural Materials as Paradigms for Superior Aerospace Systems (F.L. Hedberg and G.K. Haritos). Microstructure of an Insect Cuticle and Its Applications to Advanced Composites (S.L. Gunderson and R.C. Schiavone). Hierarchical Twin Structures and Multiple Tilings in the Nacre of Abalone Shell (M. Sarikaya et al.). The Functions of Biocomposites (S.A. Wainwright). Microstructure- Property Relations in Vertebrate Hard Tissues: Microdamage and Toughness (J.D. Curry). Role of Molecular Genetics in Polymer Materials Science (M.J. Fournier et al.). Molecular Design of Spider Silks (J.M. Gosline et al.). Biomineralization, Inorganic-Organic Interface and Crystal Engineering (S. Mann et al.). Crystal, Protein and Protein-Crystal Composites in Three Biological Materials (A. Berman et al.). Structure and Function of Magnetosomes in Magnetotactic Bacteria (R.B. Frankel). Size-Quantized Particles at Artificial Membrane Interfaces (X.K.Zhao and J.H. Fendler). Hierarchal Structures of Soft Connective Tissues--Relationship to Properties and Function (E. Baer et al.). Biomimetic Ceramics and Hard Composites (P. Calvert and J. Burdon). Processing of Ceramics by Biomimicking (I.
Costimulation via Glucocorticoid-Induced TNF Receptor in Both Conventional and CD25+ Regulatory CD4+ T Cells (2004)

The glucocorticoid-induced TNF receptor (GITR), which is a member of the TNF receptor family, is expressed preferentially at high levels on CD25+CD4+ regulatory T cells and plays a key role in the peripheral tolerance that is mediated by these cells. GITR is also expressed on conventional CD4+ and CD8+ T cells, and its expression is enhanced rapidly after activation. In this report we show that the GITR provides a potent costimulatory signal to both CD25+ and CD25- CD4+ T cells. GITR-mediated stimulation induced by anti-GITR mAb DTA-1 or GITR ligand transfectants efficiently augmented the proliferation of both CD25-CD4+ and CD25+CD4+ T cells under the limited dose of anti-CD3 stimulation. The augmentation of T cell activation was further confirmed by the enhanced cell cycle progression; early induction of the activation Ags, CD69 and CD25; cytokine production, such as IL-2, IFN-gamma, IL-4, and IL-10; anti-CD3-induced redirected cytotoxicity; and intracellular signaling, assessed by translocation of NF-kappaB components. GITR costimulation showed a potent ability to produce high amounts of IL-10, which resulted in counter-regulation of the enhanced proliferative responses. Our results highlight evidence that GITR acts as a potent and unique costimulator for an early CD4+ T cell activation.
Immunopharmacology: immunomodulation and immunotherapy (1997)

Immunopharmacology has changed dramatically over the past 25 years. Although a variety of traditional nonspecific immunosuppressive drug therapies are available for the treatment of autoimmune disease and organ transplantation rejection, with advances in cell biology and monoclonal antibody technology, a highly specific antibody can be engineered to cell surface determinants on immune cells or tumors or to neutralize inflammatory and immune mediators from an immune response. Many of these modalities are still in early phases of study for the treatment of autoimmune disease. In addition to therapies that suppress immune responses, advances in molecular biology have led to new agents and methods to enhance immune responses and correct immune deficits, such as growth factor replacement and cytokine therapies. Finally, gene therapy is a method for the long-term treatment of disorders in which a defective gene leads to disease.
Redox Pathway Leading to the Alkylation of DNA by the Anthracycline, Antitumor Drugs Adriamycin and Daunomycin (1997)

Reaction of the anthracycline, antitumor drugs adriamycin and daunomycin with the self-complementary DNA oligonucleotide GCGCGCGC, (GC)4, in the presence of the reducing agent dithiothreitol, the oxidizing agent hydrogen peroxide, or the alkylating agent formaldehyde gives a similar mixture of DNA-drug adducts. Negative ion electrospray mass spectra indicate that adduct formation involves coupling of the DNA to the anthracycline via a methylene group and that the major adduct is duplex DNA containing two molecules of anthracycline, each bound to a separate strand of the DNA via a methylene group. The source of the methylene group is formaldehyde. A molecular structure with each anthracycline intercalated at a 5'-CpG-3' site and covalently bound from its 3'-amino group to a 2-amino group of a 2'-deoxyguanosine nucleotide is proposed based upon spectral data and a relevant crystal structure. The reaction of (GC)4 with the anthracyclines and formaldehyde forms an equilibrium mixture with DNA-drug adducts which is shifted toward free DNA by dilution. The results suggest a pathway to the inhibition of transcription by reductively activated adriamycin and daunomycin. Reductive activation in the presence of oxygen yields hydrogen peroxide; hydrogen peroxide oxidizes constituents in the reaction mixture to formaldehyde; and formaldehyde couples the drug to DNA. In this regard, hydrogen peroxide reacts with adriamycin via Baeyer-Villiger reactions at the 13-position to yield 2, 3, and formaldehyde. Formaldehyde also results from hydrogen peroxide oxidation of Tris [tris(hydroxymethyl)aminomethane] present in transcription buffer and spermine, a polyamine commonly associated with DNA in vivo, presumably via the Fenton reaction.
Varicella in Hairless Guinea Pigs (1991)

A high proportion of depilated newborn or euthymic congenitally hairless adult guinea pigs develop an erythematous papular exanthem during infection with varicella-zoster virus (VZV) previously cultivated in guinea pig cell culture. Virus has been demonstrated in tissues during varicella using polymerase chain reaction amplification and nucleic acid hybridization methods. The frequency of exanthem expression can be reduced by the prophylactic administration of VZV convalescent-phase guinea pig serum. This model should prove useful for further study of VZV pathogenesis as well as for testing putative antiviral compounds.
Damage to Libraries due to Water Related Disasters (2014)

Flooding, leakage, heavy rains, hurricanes, activation of fire sprinklers due to fire are some of the reasons due to which water can enter library premises. It can damage library resources and infrastructure as well as disrupt services for a long time. The paper describes the ways libraries can be prepared for such disasters as well as how to treat resources damaged due to such disasters.
Analysis of Spread Spectrum System Parameters for Design of Hidden Transmission (1995)

A short analysis of spread spectrum communication system is performed with respect to the determination of its fundamental system parameters for transmitted signal hidden in the noise. The paper shows dependence of processing gains on the correlation circuits at the receiver side. The distance, from which the transmitter signal is hidden in noise, depends on the spread spectrum factor and the transmitted power. At a given interference power density and at a given requirement of transmitted signal hiding we can calculate the spreading factor of system. A processing gain of spread spectrum system determines a depth of signal hiding in the noise. A transmission range of spread spectrum communication system is given by the transmitted power and the processing gain of the system.
Epitope Mapping: B ‐cell Epitopes (2007)

Abstract Immunoglobulin molecules are folded to present a surface structure complementary to a surface feature on the antigen – the epitope is this feature of the antigen. Epitope mapping is the process of locating the antibody‐binding site on the antigen, although the term is also applied more broadly to receptor–ligand interactions unrelated to the immune system.
Semiconductor laser crystallization of a-Si:H (2003)

Results of semiconductor laser crystallization of a-Si:H on transparent conducting fluoride doped tin oxide coated glass are discussed. A-Si:H films were prepared by plasma enhanced chemical vapor deposition. Laser crystallized films of a-Si:H were characterized by X-ray diffraction and optical microscopy. Semiconductor laser crystallization process as compared to well-established excimer laser offers low cost large area technology for solar cell, display and other applications. Longer wavelength of diode lasers (805 nm) allows light to penetrate deeper in the films for crystallization of thicker films required for enhanced light absorption.
Rapid Turnover of Connexin43 in the Adult Rat Heart (1998)

Remodeling of the distribution of gap junctions is an important feature of anatomic substrates of arrhythmias in patients with healed myocardial infarcts. Mechanisms underlying this process are poorly understood but probably involve changes in gap junction protein (connexin) synthesis, assembly into channels, and degradation. The half-life of the principal cardiac gap junction protein, connexin43 (Cx43), is only 1.5 to 2 hours in primary cultures of neonatal myocytes, but it is unknown whether rapid turnover of Cx43 occurs in the adult heart or is unique to disaggregated neonatal myocytes that are actively reestablishing connections in vitro. To characterize connexin turnover dynamics in the adult heart and to elucidate its potential role in remodeling of gap junctions, we measured Cx43 turnover kinetics and characterized the proteolytic pathways involved in Cx43 degradation in isolated perfused adult rat hearts. Hearts were labeled for 40 minutes with Krebs-Henseleit buffer containing [35S]methionine, and then chase perfusions were performed with nonradioactive buffer for 0, 60, 120, and 240 minutes. Quantitative immunoprecipitation assays of Cx43 radioactivity in 4 hearts at each time point yielded a monoexponential decay curve indicating a Cx43 half-life of 1.3 hours. Proteolytic pathways responsible for Cx43 degradation were elucidated by perfusing isolated rat hearts for 4 hours with specific inhibitors of either lysosomal or proteasomal proteolysis. Immunoblot analysis demonstrated significant increases ( approximately 30%) in Cx43 content in hearts perfused with either lysosomal or proteasomal pathway inhibitors. Most of the Cx43 in hearts perfused with lysosomal inhibitors consisted of phosphorylated isoforms, whereas nonphosphorylated Cx43 accumulated selectively in hearts perfused with a specific proteasomal inhibitor. These results indicate that Cx43 turns over rapidly in the adult heart and is degraded by multiple proteolytic pathways. Regulation of Cx43 degradation could play an important role in gap junction remodeling in response to cardiac injury.
The Unfolded Protein Response: A Novel Component of the Hypoxic Stress Response in Tumors (2005)

Hypoxia is a physiologically important endoplasmic reticulum (ER) stress that is present in all solid tumors. Numerous clinical studies have shown that tumor hypoxia predicts for decreased local control, increased distant metastases, and decreased overall survival in a variety of human tumors. Hypoxia selects for tumors with an increased malignant phenotype and increases the metastatic potential of tumor cells. Tumor cells respond to hypoxia and ER stress through the activation of the unfolded protein response (UPR). The UPR is an adaptive response to increase cell survival during ER stress. XBP-1 is a critical transcriptional regulator of this process and is required for tumor growth. Pancreatic ER kinase (PKR-like ER kinase) regulates the translational branch of the UPR and is also important in the growth of tumors. Although the exact mechanism has yet to be elucidated, recent data suggest that the UPR affects tumor growth through protection from apoptosis and may influence angiogenic signaling pathways. Targeting various components of the UPR is a promising therapeutic strategy. Understanding the relationship between hypoxia, the UPR, and tumor growth is crucial to improving current cancer therapies.
HLA-DR Restricted Peptide Candidates for Bee Venom Immunotherapy (2000)

T cell epitopes containing peptides have been recently proposed as an alternative to conventional immunotherapy of allergic diseases because they are expected to be better tolerated than allergen extracts. A principal limitation to their clinical use is that they present an important diversity, which primarily results from the polymorphism of HLA class II molecules. In Caucasian populations, however, seven alleles of the most expressed molecules (namely DRB1*0101, DRB1*0301, DRB1*0401, DRB1*0701, DRB1*1101, DRB1*1301, and DRB1*1501) predominate. Peptides from allergens that would efficiently bind to them should be potential candidates for specific immunotherapy. In this paper, we have determined the peptides present in the major bee venom allergen by investigating the capacity of synthetic peptides that encompass its whole sequence to bind to each allele. Several efficient binders have been identified and are either allele-specific or common to several HLA-DR molecules. Interestingly enough, the 81-97 sequence is universal in the sense that it binds to all studied molecules. This sequence is surrounded by several active regions, which make the 76-106 sequence particularly rich of binding determinants and a good candidate for specific immunotherapy. Statistical analyses of the binding data also provide an overview of the preponderant HLA-DR alleles specificity.
Error analysis of optical matched filter (1966)

The degradation of performance of optical matched filters due to translation and rotation is examined. Included is a similar discussion due to variation in signal sizes. A rectangular signal is employed in carrying out the analysis. As a result of which the estimation of the allowed position errors in distinguishing signals of different sizes can be made.
Integrating diverse knowledge sources in text recognition (1983)

A new algorithm for text recognition that corrects character substitution errors in words of text is presented. The search for a correct word effectively integrates three knowledge sources: channel characteristics, bottom-up context, and top-down context. Channel characteristics are used in the form of probabilities that observed letters are corruptions of other letters; bottom-up context is in the form of the probability of a letter when the previous letters of the word are known; and top-down context is in the form of a lexicon. A one-pass algorithm is obtained by merging a previously known dynamic programming algorithm to compute the maximum a posteriori probability string (known as the Viterbi algorithm) with searching a lexical trie. Analysis of the computational compexity of the algorithm and results of experimentation with a PASCAL implementation are presented.
A review of the natural history of cervical intraepithelial neoplasia. (2002)

Cervical Intraepithelial Neoplasia (CIN) is a premalignant lesion of cervical squamous cell carcinoma which over time may persist unchanged, regress to normal or a lesser grade of CIN, or progress to a higher grade of CIN or invasive carcinoma. Rates of progression correlate directly with the CIN grade. Human Papilloma Virus (HPV) detection is a significant determinant of CIN regardless of grade. Studies of risk factor profiles, cytogenetic abnormalities, cell proliferation indices, cell cycle and senescence control, oncogene and tumor suppressor gene expression, protein expression, and HPV status have been conducted to identify determinants of CIN I and CIN II/III and predictors of CIN 1 progression. Differences in these attributes suggest that CIN I is a sexually transmitted, productive HPV infection, whereas CIN II/III is a dysplastic lesion resulting from repeated exposure to a sexually transmitted HPV and possibly an additional agent. HPV16 positivity and increased viral load in some earlier studies were predictive of prevalent CIN II/III. More recent studies with more sensitive HPV assays did not corroborate these findings. The role of cigarette smoking is controversial and requires additional study. Accumulating evidence suggests that high risk HPV DNA detection and persistence are predictive of CIN I progressing to CIN II/III. Other possibilities are persistence of a high risk HPV variant, altered cell immunity, and cigarette and oral contraceptive use. Possible biomarkers include aneuploidy, aneusomy of chromosomes 1 and 3, Ras and bcl-2 oncogene over expression, and cytokeratin 13 protein under-expression.
Simple and efficient generation in vitro of nested deletions and inversions: Tn5 intramolecular transposition (1998)

We have exploited the intramolecular transposition preference of the Tn 5 in vitro transposition system to test its effectiveness as a tool for generation of nested families of deletions and inversions. A synthetic transposon was constructed containing an ori, an ampicillin resistance (Ampr) gene, a multi-cloning site (MCS) and two hyperactive end sequences. The donor DNA that adjoins the transposon contains a kanamycin resistance (Kanr) gene. Any Amprreplicating plasmid that has undergone a transposition event (Kans) will be targeted primarily to any insert in the MCS. Two different size targets were tested in the in vitro system. Synthetic transposon plasmids containing either target were incubated in the presence of purified transposase (Tnp) protein and transformed. Transposition frequencies (Ampr/Kans) for both targets were found to be 30-50%, of which >95% occur within the target sequence, in an apparently random manner. By a conservative estimate 10(5) or more deletions/inversions within a given segment of DNA can be expected from a single one-step 20 microl transposition reaction. These nested deletions can be used for structure-function analysis of proteins and for sequence analysis. The inversions provide nested sequencing templates of the opposite strand from the deletions.
Facile Trypsin Immobilization in Polymeric Membranes for Rapid, Efficient Protein Digestion (2010)

Sequential adsorption of poly(styrene sulfonate) and trypsin in nylon membranes provides a simple, inexpensive method to create stable, microporous reactors for fast protein digestion. The high local trypsin concentration and short radial diffusion distances in membrane pores facilitate proteolysis in residence times of a few seconds, and the minimal pressure drop across the thin membranes allows their use in syringe filters. Membrane digestion and subsequent MS analysis of bovine serum albumin provide 84% sequence coverage, which is higher than the 71% coverage obtained with in-solution digestion for 16 h or the <50% sequence coverages of other methods that employ immobilized trypsin. Moreover, trypsin-modified membranes digest protein in the presence of 0.05 wt % sodium dodecyl sulfate (SDS), whereas in-solution digestion under similar conditions yields no peptide signals in mass spectra even after removal of SDS. These membrane reactors, which can be easily prepared in any laboratory, have a shelf life of several months and continuously digest protein for at least 33 h without significant loss of activity.