gebhart/patrepeval huggingface dataset:
Data Structures, Algorithms and Applications in Java (1998)

Sahni's Data Structures, Algorithms, and Applications in Java is designed to be used in a second course in computer science (CS2). Using Java, this book provides comprehensive coverage of the fundamental data structures, making it an excellent choice for a CS2 course. The author has made this book student-friendly through intuitive discussion, real-world, applications and a gentle introduction. Sahni is unique in providing several real-world applications for each data structure presented in the book. These applications come from such areas as sorting, compression and coding, and image processing. These applications give students a flavor for the sorts of things they will be able to do with the data structures that they are learning. Almost 1,000 exercises in this text serve to reinforce concepts and get students applying what they are learning. Sahni's text is also accompanied by a web site containing all the programs in the book, as well as sample data, generated output, solutions to selected exercises, and enhanced discussion of selected material in the text.
Effectiveness of Toyota Process Redesign in Reducing Thyroid Gland Fine-Needle Aspiration Error (2006)

Our objective was to determine whether the Toyota Production System process redesign resulted in diagnostic error reduction for patients who underwent cytologic evaluation of thyroid nodules. In this longitudinal, nonconcurrent cohort study, we compared the diagnostic error frequency of a thyroid aspiration service before and after implementation of error reduction initiatives consisting of adoption of a standardized diagnostic terminology scheme and an immediate interpretation service. A total of 2,424 patients underwent aspiration. Following terminology standardization, the false-negative rate decreased from 41.8% to 19.1% (P = .006), the specimen nondiagnostic rate increased from 5.8% to 19.8% (P < .001), and the sensitivity increased from 70.2% to 90.6% (P < .001). Cases with an immediate interpretation had a lower noninterpretable specimen rate than those without immediate interpretation (P < .001). Toyota process change led to significantly fewer diagnostic errors for patients who underwent thyroid fine-needle aspiration.
Prevalence of mycoplasmas and immune responses to Mycoplasma bovis in feedlot calves. (1983)

Microbiological cultural, cytologic, and immunologic observations were made on 30 calves. The eyes, nares, and bronchioalveolar region were subjected to microbiological cultural examination for mycoplasmas. Four of the examinations of 30 eyes, 15 of those of 30 nasal tissues, and 25 of those of the 30 bronchioalveolar regions from the 30 calves were positive for mycoplasmas. Mycoplasma bovis and M bovirhinis were the most prevalent species. Cytologic examinations of peripheral blood and bronchioalveolar washes did not show pathologic changes. Results of indirect hemagglutination, enzyme-linked immunosorbent assay, lymphocyte-stimulation tests on peripheral blood cells, and skin testing demonstrated only a low prevalence of immune recognition of M bovis. Infection and immune response were studied in 3 calves for 10 weeks before, and for 4 weeks after, intratracheal administration of live M bovis.
Significance of macrophage chemoattractant protein-1 in macrophage recruitment, angiogenesis, and survival in human breast cancer. (2000)

Tumor cells stimulate the formation of stroma that secretes various mediators pivotal for tumor growth, including growth factors, cytokines, and proteases. However, little is known about the local regulation of these soluble mediators in the human tumor microenvironment. In this study, the local expression of cytokines, chemokines, and angiogenic factors was investigated in primary breast cancer tissue. The concentrations of interleukin (IL)-1, IL-4, IL-6, IL-10, IL-12, tumor necrosis factor (TNF)-alpha, IFN-gamma, IL-8, macrophage chemoattractant protein (MCP)-1, epithelial-neutrophil activating peptide-78, vascular endothelial growth factor, and thymidine phosphorylase (TP) were measured in 151 primary breast cancer extracts by ELISA. Tumor-associated macrophages (TAMs) were also examined by immunohistochemistry with anti-CD68 antibodies. The correlation between soluble mediators and the relationship between TAM count and soluble mediators were evaluated. MCP-1 concentration was correlated significantly with the level of vascular endothelial growth factor, TP, TNF-alpha, and IL-8, which are potent angiogenic factors. IL-4 concentration was correlated significantly with IL-8 and IL-10. On the other hand, an inverse association was observed between TP and IL-12. The level of MCP-1 was associated significantly with TAM accumulation. In the immunohistochemical analysis, MCP-1 expression was observed in both infiltrating macrophages and tumor cells. Prognostic analysis revealed that high expression of MCP-1, as well as of VEGF, was a significant indicator of early relapse. These findings indicate that interaction between the immune network system and angiogenesis is important for progression of human breast cancer, and that MCP-1 may play an important role in the regulation of angiogenesis and the immune system.
A five-coordinate copper(II) perchlorate complex with tris(N-methylbenzimidazol-2-ylmethyl)amine and salicylate (2009)

A five-coordinate copper(II) complex with the tripod ligand tris(N-methylbenzimidazol-2-ylmethyl)amine (Mentb) and salicylate, with the composition [Cu(Mentb) (salicylate)](ClO4) · 2DMF, was synthesized and characterized by elemental and thermal analyses, electrical conductivity, IR and UV-Vis spectral measurements. The crystal structure of the complex has been determined by single-crystal X-ray diffraction. The Cu(II) is five-coordinate with four N atoms from the Mentb ligand and an O atom of the monodentate salicylate ligand. The N4O donors are in a distorted trigonal-bipyramid geometry. Cyclic voltammograms indicate a quasireversible Cu2+/Cu+ couple. The X-band EPR spectrum of the complex confirms the trigonal-bipyramidal structure with g∥ < g ⊥ and a very small value of A∥ (41 × 10−4 cm−1).
Metal Schottky barrier contacts to alpha 6H-SiC (1992)

Formation of Schottky barrier contacts to n-type 6H-SiC for a number of metals chosen to include a variety of physical and chemical properties has been investigated. The metals (Pd, Au, Ag, Tb, Er, Mn, Al, and Mg) were deposited onto room temperature surfaces terminated with a submonolayer coverage of oxygen. The metal/6H-SiC interface chemistry and Schottky barrier height φB during contact formation were obtained with x-ray photoemission spectroscopy; the electrical properties of subsequently formed thick contacts were characterized by current-voltage and capacitance-voltage techniques. The o/B values for these metals extend over a wide 1.3 eV range. To a varying degree φB depends on the 6H-SiC crystal face (Si vs C). Mg and Al (Si face of latter) have φB=0.3 eV, a value which is suitable for nonalloyed ohmic contacts.
Imaging Oncogene Expression (2003)

In 2003, approximately 39,800 women in the US will die from breast cancer. Mammography and physical examination miss up to 40% of early breast cancers. Moreover, if an abnormality is found, an invasive diagnostic procedure must still be performed to determine if the breast contains atypia or cancer, even though approximately 85% of abnormalities are benign. Scintigraphic imaging of gene expression in vivo by noninvasive means could direct physicians to appropriate targets for intervention at the onset of disease and thereby significantly impact patient management. Until now, no method has been available to image specific overexpressed oncogene mRNAs in vivo by scintigraphic imaging. We hypothesize that gamma-emitting Tc-99m-PNA-peptides can be taken up by human ER+ and ER- breast cancer xenografts, hybridize to complementary mRNA targets in those cells, and concentrate sufficiently in tumor tissue to allow noninvasive imaging of oncogene overexpression. To prepare the probes, peptide analogs of insulin-like growth factor 1 (IGF1) were extended from a solid support by Fmoc coupling. Peptide nucleic acid (PNA) dodecamers antisense to CCND1 and MYC mRNAs were then extended from the N-terminus of IGF1, followed by a chelator peptide, using Fmoc coupling for all residues. The cysteine thiols were cyclized on the solid support, either before or after PNA extension. This simplified synthetic approach allows preparation of a variety of multipeptide disulfide-bridged PNA chimeras. A chelating peptide-PNA chimera antisense to MYC mRNA was then labeled efficiently with Tc-99m, yielding a single product. Tissue distribution studies of antisense and mismatch chimeras at 4 h and 24 h after administration displayed modest accumulation in the liver and kidneys, with appreciable levels in tumors. This result enables testing of Tc-99m-peptide-PNA probes to image gene expression in tumors.
Response of digestive gland cells of freshwater mussel Unio tumidus to phenolic compound exposure in vivo (2006)

The exposure of freshwater mussels Unio tumidus to phenolic compounds (tannic, ellagic and gallic acid) in vivo caused changes in proteins and DNA function of digestive gland cells. The mussels were exposed to various concentrations of tested polyphenols (60, 200 and 500 microM) for 24 and 48 h and their antioxidant and pro-oxidant effects were determined. The number of SH-groups was quantified spectrophotometrically using Ellman's reagent. Oxidative modification of proteins increased in the digestive gland cells in a dose- and time-dependent manner. The level of nuclear DNA damage was investigated using the comet assay. The results revealed that polyphenolic acids induce single and double-strand breaks in DNA. The highest changes were observed for tannic and gallic acids and the smallest ones for ellagic acid. 1h of DNA repair process was also studied using the same method. The data obtained in this experiment demonstrate that the most effective DNA repair occurs in the cells exposed to phenolic compounds for 24h. A longer incubation (up to 48 h) does not decrease the capacity of the repair mechanism. The antioxidant activity of the tested phenols was analyzed spectrofluorimetrically using a fluorescence probe DCFH-DA (dichlorofluorescein-diacetate). The experimental data showed that the tested acids can act as antioxidants when used at higher doses (200 and 500 microM) against the reactive oxygen species present in the digestive gland cells. The most effective was ellagic acid, also applied at the smallest dose of 60 microM, in comparison with tannic and gallic acids. In conclusion, our results demonstrate that chosen water-soluble polyphenols, which are located in various plant tissues and are also found in the aquatic environment, can influence organisms living in the water. They can be exposed to these chemicals that cause morphological alterations and changes in certain physiological processes in their organs (i.e. digestive gland cells of bivalve molluscs).
A Linearized Cascode CMOS Power Amplifier (2006)

In this paper, an RF predistorter linearizer compatible with a CMOS process is proposed. The predistorter uses a diode connected MOSFET as a nonlinearity generation circuit. A negative or positive AM-PM characteristic is obtained from the predistorter by inserting a capacitor or an inductor in parallel with the predistorter. A 5.8 GHz cascode CMOS power amplifier was designed using a 0.18-mum 1P6M mixed-mode CMOS process and a predistorter was customized for the cascode power amplifier and integrated with it. The gain and phase distortion of the power amplifier were compensated and the simulation result of the cascode power amplifier shows a 29.3-dB improvement in the third order inter-modulation distortion when the predistorter is turned on.
Restriction and enhancement of human immunodeficiency virus type 1 replication by modulation of intracellular deoxynucleoside triphosphate pools (1994)

Human immunodeficiency virus type 1 (HIV-1) replication is shown to be sensitive to the intracellular concentration of deoxynucleoside triphosphate substrates. Addition of thymidine to established cell lines resulted in a dramatic reduction of virus production. The effect could be substantially alleviated by addition of deoxycytidine, which, alone, enhanced viral titers by a factor of 2 to 3. Hydroxyurea treatment abolished HIV-1 replication in peripheral blood mononuclear cells and could be reversed by deoxyadenosine. These data show that HIV-1 replication occurs under suboptimal DNA precursor conditions.
The Ribosomal Database Project (RDP) (1996)

The Ribosomal Database Project (RDP) is a curated database that offers ribosome-related data, analysis services and associated computer programs. The offerings include phylogenetically ordered alignments of ribosomal RNA (rRNA) sequences, derived phylogenetic trees, rRNA secondary structure diagrams and various software for handling, analyzing and displaying alignments and trees. The data are available via anonymous ftp (rdp.life.uiuc.edu), electronic mail (server@rdp.life.uiuc.edu), gopher (rdpgopher.life.uiuc.edu) and World Wide Web (WWW)(http://rdpwww.life.uiuc.edu/). The electronic mail and WWW servers provide ribosomal probe checking, screening for possible chimeric rRNA sequences, automated alignment and approximate phylogenetic placement of user-submitted sequences on an existing phylogenetic tree.
Protecting browsers from DNS rebinding attacks (2009)

DNS rebinding attacks subvert the same-origin policy of browsers, converting them into open network proxies. Using DNS rebinding, an attacker can circumvent organizational and personal firewalls, send spam email, and defraud pay-per-click advertisers. We evaluate the cost effectiveness of mounting DNS rebinding attacks, finding that an attacker requires less than $100 to hijack 100,000 IP addresses. We analyze defenses to DNS rebinding attacks, including improvements to the classic “DNS pinning,” and recommend changes to browser plug-ins, firewalls, and Web servers. Our defenses have been adopted by plug-in vendors and by a number of open-source firewall implementations.
Rituximab-mediated antibody-dependent cellular cytotoxicity against neoplastic B cells is stimulated strongly by interleukin-2. (2003)

Primary leukemic cells are more resistant than cell lines to rituximab- and NK cell-mediated ADCC but short-term exposure to IL-2 or long-term expansion of NK cells in vitro may provide effective tools to improve the therapeutic activity of rituximab.
High electroluminescence of the ZnS:Mn nanoparticle/cyanoethyl-resin polymer/single-walled carbon nanotube composite using the tandem structure (2012)

The EL performance of the tandem structured phosphor/polymer/SWCNT composite was greatly increased by structural and material effects, which led to increased tunneling charge carriers into phosphor, resulting in improved luminance. The tandem structured composite EL device exhibited a 1570% increase in the luminance compared to the raw phosphor EL device.
Origin of the polycomb repressive complex 2 and gene silencing by an E(z) homolog in the unicellular alga Chlamydomonas (2010)

Polycomb group proteins play an essential role in the maintenance of cell identity and the regulation of development in both animals and plants. The Polycomb Repressive Complex 2 (PRC2) is involved in the establishment of transcriptionally silent chromatin states, in part through its ability to methylate lysine 27 of histone H3 by the Enhancer of zeste [E(z)] subunit. The absence of PRC2 in unicellular model fungi and its function in the repression of genes vital for the development of higher eukaryotes led to the proposal that this complex may have evolved together with the emergence of multicellularity. However, we report here on the widespread presence of PRC2 core subunits in unicellular eukaryotes from the Opisthokonta, Chromalveolata and Archaeplastida supergroups. To gain insight on the role of PRC2 in single celled organisms, we characterized an E(z) homolog, EZH, in the green alga Chlamydomonas reinhardtii. RNAi-mediated suppression of EZH led to defects in the silencing of transgenes and retrotransposons as well as to a global increase in histone post-translational modifications associated with transcriptional activity, such as trimethylation of histone H3 lysine 4 and acetylation of histone H4. On the basis of the parsimony principle, our findings suggest that PRC2 appeared early in eukaryotic evolution, even perhaps in the last unicellular common ancestor of eukaryotes. One of the ancestral roles of PCR2 may have been in defense responses against intragenomic parasites such as transposable elements, prior to being co-opted for lineage specific functions like developmental regulation in multicellular eukaryotes.
Characterization of a mammalian mutant with a camptothecin-resistant DNA topoisomerase I. (1987)

DNA topoisomerase I was purified to near homogeneity from a clonal line of human lymphoblastic leukemia cells, RPMI 8402, that is resistant to camptothecin, a cytotoxic alkaloid from Camptotheca acuminata, and compared with that of the parent wild-type cells. As assayed by relaxation of the supercoiled plasmid DNA and by formation of enzyme-linked DNA breaks, the purified enzyme from the resistant cells was shown to be greater than 125-fold as resistant to camptothecin as the wild-type enzyme, comparable to a cellular resistance index of about 300. Therefore, the cellular resistance appears to be due to the resistance of the enzyme. The amount of the immunoreactive enzyme protein in whole extract appeared to be reduced to less than half that of the wild-type enzyme. These results establish that DNA topoisomerase I is the cellular target of camptothecin and that DNA topoisomerase I is essential for the survival of mammalian cells.
Small and Stable Sulfobetaine Zwitterionic Quantum Dots for Functional Live-Cell Imaging (2010)

We have developed a novel surface coating for semiconductor quantum dots (QDs) based on a heterobifunctional ligand that overcomes most of the previous limits of these fluorescent probes in bioimaging applications. Here we show that QDs capped with bidentate zwitterionic dihydrolipoic acid-sulfobetaine (DHLA-SB) ligands are a favorable alternative to polyethylene glycol-coated nanoparticles since they combine small sizes, low nonspecific adsorption, preserved optical properties, and excellent stability over time and a wide range of pH and salinity. Additionally, these QDs can easily be functionalized with biomolecules such as streptavidin (SA) and biotin. We applied streptavidin-functionalized DHLA-SB QDs to track the intracellular recycling of cannabinoid receptor 1 (CB1R) in live cells. These QDs selectively recognized the pool of receptors at the cell surface via SA-biotin interactions with negligible nonspecific adsorption. The QDs retained their optical properties, allowing the internalization of CB1R into endosomes to be followed. Moreover, the cellular activity was apparently unaffected by the probe.
Characterization of Blood Properties from Coagulating Blood of Different Hematocrits Using Ultrasonic Backscatter and Attenuation (2006)

The influence of hematocrit on the change of blood properties during coagulating was extensively investigated using ultrasonic integrated backscatter and attenuation. Measurements were performed with porcine blood at hematocrits ranging from 25 to 55% using a 10 MHz transducer. Results showed that both integrated backscatter and attenuation are able to sensitively differentiate various stages of blood properties during coagulating. The slopes of integrated backscatter (Sr, dB/S) and attenuation (αr, dB·cm-1·MHz-1·mS-1) are increased relative to hematocrit. The best fits for Sr and αr as a function of hematocrit (H) equal to Sr=0.0357+1.62e-0.108H and αr=0.0281+0.003H, respectively. Variations of clotting time (Ts) and reaction time (Tα), estimated respectively from ultrasonic integrated backscatter and attenuation, associated with clot formation are also increased with hematocrit. This study demonstrates that blood hematocrit is a substantial factor affecting viscosity and backscattering properties of blood during coagulation capable of being discerned by ultrasonic backscattering and attenuation.
Approximate String Joins in a Database (Almost) for Free (2001)

String data is ubiquitous, and its management has taken on particular importance in the past few years. Approximate queries are very important on string data especially for more complex queries involving joins. This is due, for example, to the prevalence of typographical errors in data, and multiple conventions for recording attributes such as name and address. Commercial databases do not support approximate string joins directly, and it is a challenge to implement this functionality efficiently with user-defined functions (UDFs). In this paper, we develop a technique for building approximate string join capabilities on top of commercial databases by exploiting facilities already available in them. At the core, our technique relies on matching short substrings of length , called -grams, and taking into account both positions of individual matches and the total number of such matches. Our approach applies to both approximate full string matching and approximate substring matching, with a variety of possible edit distance functions. The approximate string match predicate, with a suitable edit distance threshold, can be mapped into a vanilla relational expression and optimized by conventional relational optimizers. We demonstrate experimentally the benefits of our technique over the direct use of UDFs, using commercial database systems and real data. To study the I/O and CPU behavior of approximate string join algorithms with variations in edit distance and -gram length, we also describe detailed experiments based on a prototype implementation. Permission to copy without fee all or part of this material is granted provided that the copies are not made or distributed for direct commercial advantage, the VLDB copyright notice and the title of ...
Isolation and characterization of an active compound from black soybean [Glycine max (L.) Merr.] and its effect on proliferation and differentiation of human leukemic U937 cells (2001)

Black soybean [Glycine max (L.) Merr.] has been used as a health food and herb in China for hundreds of years. In the present study, we purified a unique polysaccharide component from black soybean (PSBS) and found that it indirectly inhibits proliferation and induces differentiation of human leukemic U937 cells via activation of mononuclear cells (MNCs). We prepared conditioned media (MNC-CM) by incubating MNCs from human peripheral blood with or without PSBS (PSBS-MNC-CM and normal MNC-CM, respectively). Treatment of human leukemic U937 cells with PSBS-MNC-CM significantly inhibited proliferation of U937 cells, reducing their growth by 98.5%. Furthermore, PSBS-MNC-CM induced U937 cells to differentiate into mature monocytes/macrophages (83% by morphological examination and 90% by the nitroblue tetrazolium test). Neither PSBS alone nor normal MNC-CM had such effects. The molecular weight of PSBS was about 480 000 by gel filtration. Structural analysis of PSBS revealed that (1,6)-alpha-D-glucan might be its major active component. Our results suggest that the PSBS may inhibit proliferation and induce differentiation in human leukemic U937 cells by activating the immune response of MNCs.