gebhart/patrepeval huggingface dataset:
TWO DIMENSIONAL AIR BUBBLE PLUME IN UPWARD FLOW (1988)

A discharge of air bubbles into water in a aeration tank generates a turbulent air bubble plume in a spiral flow. This paper discribes the mechanics of the air-bubble plume in a upward flow instead of the spiral flow. We measured the mean velocities and the streamwise component of the turbulent fluctuations with a miniature propeller current meter. It is found that the interaction of air bubbles plays very important role in the region close to the line source. The results of the analyses by the use of moment transformations for equations of momentum and volume conservation of bubbles are compared with experimental data.
Decreased Immunologic Responsiveness Following Intensified Vaginal Immunization Against Urinary Tract Infection (1990)

In an attempt to further increase the protective effect of vaginal immunization against urinary tract infections in Cynomolgus monkeys, the immunogen of killed E. coli was given more times, in larger amounts, and with the adjuvant MDP. Instead of increasing the protective effect, no protective effect on induced cystitis was observed. In addition, rises in urinary and serum immunoglobulins previously observed after vaginal immunization and induced cystitis were lessened. These observations appear to correspond with the classical concepts of immunologic unresponsiveness.
Polyclonal anti-idiotypic antibodies as internal images of dopamine. Applications for biochemical and morphological studies of DA receptors in the rat brain. (1991)

Polyclonal anti-idiotypic antiserum raised against both rabbit and monoclonal anti-dopamine (DA) antibodies was produced in rabbits. It was characterized for its specificity and was shown to (1) inhibit the binding of both polyclonal and monoclonal idiotypic anti-DA antibodies directed to immobilized DA conjugates; (2) inhibit the binding of (3H) DA to rat brain membranes; (3) to cross-react with a peptide extracted from a neuroblastoma cell line (NCB-20), known to express functional DA receptors. Finally, immunocytochemical studies were performed on paraformaldehyde-fixed rat brain. Anti-idiotypic antibodies were used to visualize the cellular and subcellular distribution of DA receptor binding sites in the striatum, a region that contains both D1 and D2 receptors subtypes. Under the electron microscope, the immune reaction product was observed to be concentrated in postsynaptic sites belonging mainly to dendritic spines, while presynaptic structures were sparsely labeled.
In vitro assessment of the effects of vedolizumab binding on peripheral blood lymphocytes (2013)

Vedolizumab (VDZ) is a humanized monoclonal antibody in development for the treatment of inflammatory bowel disease. VDZ binds to the α4β7 integrin complex and inhibits its binding to mucosal addressin cell adhesion molecule-1 (MAdCAM-1), thus preventing lymphocyte extravasation to gut mucosal tissues. To understand whether VDZ has additional effects that may affect its overall safety as a therapeutic molecule, we examined other potential actions of VDZ. In vitro assays with human peripheral blood lymphocytes demonstrated that VDZ fails to elicit cytotoxicity, lymphocyte activation, and cytokine production from memory T lymphocytes and does not interfere with the suppressive ability of regulatory T cells. Furthermore, we demonstrated that VDZ induces internalization of α4β7 and that the integrin is rapidly re-expressed and fully functional after VDZ withdrawal. These studies provide insight into the mechanisms underlying the observed safety profile of VDZ in clinical trials.
Impact of Major Cardiovascular Disease Risk Factors, Particularly in Combination, on 22-Year Mortality in Women and Men (1998)

Combinations of major CVD risk factors place women and men at high relative, absolute, and absolute excess risk of coronary heart disease, CVD, and all-cause mortality. These findings support the value of (1) measurement of major CVD risk factors, especially in combination, for assessing long-term mortality risk and (2) current advice to match treatment intensity to the level of CVD risk in both women and men.
Estrogen Receptor Subtype-Selective Ligands:  Asymmetric Synthesis and Biological Evaluation of cis- and trans-5,11-Dialkyl- 5,6,11,12-tetrahydrochrysenes (1999)

We have recently reported that racemic 5,11-cis-diethyl-5,6,11, 12-tetrahydrochrysene-2,8-diol (THC, rac-2b) acts as an agonist on estrogen receptor alpha (ERalpha) and as a complete antagonist on estrogen receptor beta (ERbeta) (Sun et al. Endocrinology 1999, 140, 800-804). To further investigate this novel ER subtype-selective estrogenic activity, we have synthesized a series of cis- and trans-dialkyl THCs. cis-Dimethyl, -diethyl, and -dipropyl THCs 2a-c were prepared in a highly enantio- and diastereoselective manner by the acyloin condensation of enantiomerically pure alpha-alkyl-beta-arylpropionic esters, followed by a Lewis acid-mediated double cyclization under conditions of minimal epimerization. ERalpha and ERbeta binding affinity of both cis and trans isomers of dimethyl, diethyl, and dipropyl THCs was determined in competitive binding assays, and their transcriptional activity was determined in reporter gene assays in mammalian cells. Nearly all THCs examined were found to be affinity-selective for ERbeta. All these THCs are agonists on ERalpha, and THCs with small substituents are agonists on both ERalpha and ERbeta. As substituent size was increased, ERbeta-selective antagonism developed first in the (R,R)-cis enantiomer series and finally in the trans diastereomer and (S,S)-cis enantiomer series. The most potent and selective ligand was identified as (R,R)-cis-diethyl THC 2b, which mimicked the ERbeta-selective antagonist character of racemic cis-diethyl THC 2b. This study illustrates that the antagonist character in THC ligands for ERbeta depends in a progressive way on the size and geometric disposition of substituent groups and suggests that the induction of an antagonist conformation in ERbeta can be achieved with these ligands with less steric perturbation than in ERalpha. Furthermore, antagonists that are selectively effective on ERbeta can have structures that are very different from the typical antiestrogens tamoxifen and raloxifene, which are antagonists on both ERalpha and ERbeta.
Immunoisolation of Caveolae with High Affinity Antibody Binding to the Oligomeric Caveolin Cage (1999)

Defining the molecular composition of caveolae is essential in establishing their molecular architecture and functions. Here, we identify a high affinity monoclonal antibody that is specific for caveolin-1alpha and rapidly binds caveolin oligomerized around intact caveolae. We use this antibody (i) to develop a new simplified method for rapidly isolating caveolae from cell and tissue homogenates without using the silica-coating technology and (ii) to analyze various caveolae isolation techniques to understand how they work and why they yield different compositions. Caveolae are immunoisolated from rat lung plasma membrane fractions subjected to mechanical disruption. Sonication of plasma membranes, isolated with or without silica coating, releases caveolae along with other similarly buoyant microdomains and, therefore, requires immunoisolations to purify caveolae. Shearing of silica-coated plasma membranes provides a homogeneous population of caveolae whose constituents (i) remain unchanged after immunoisolation, (ii) all fractionate bound to the immunobeads, and (iii) appear equivalent to caveolae immunoisolated after sonication. The caveolae immunoisolated from different low density fractions are quite similar in molecular composition. They contain a subset of key signaling molecules (i.e. G protein and endothelial nitric oxide synthase) and are markedly depleted in glycosylphosphatidylinositol-anchored proteins, beta-actin, and angiotensin-converting enzyme. All caveolae isolated from the cell surface of lung microvascular endothelium in vivo appear to be coated with caveolin-1alpha. Caveolin-1beta and -2 can also exist in these same caveolae. The isolation and analytical procedures as well as the time-dependent dissociation of signaling molecules from caveolae contribute to key compositional differences reported in the literature for caveolae. This new, rapid, magnetic immunoisolation procedure provides a consistent preparation for use in the molecular analysis of caveolae.
D-penicillamine induced myasthenia gravis: clinical, serological and genetic findings. (1993)

Eight cases of D-penicillamine (DP) induced myasthenia gravis (MG) are presented. Seven patients were being treated for rheumatoid arthritis (RA) and one for scleroderma. The mean duration of DP treatment until the myasthenic symptoms developed ranged from 2-8 months. The DP dose reached 500 mg daily. It was found that the clinical and immunological findings were almost similar to those of idiopathic MG, but were less severe. All patients had increased titers of acetylcholine receptor antibodies in their sera. Discontinuation of D-penicillamine resulted in the complete resolution of myasthenic symptoms after 2-6 months. One patient required ventilation, immunosuppressive therapy and plasma exchange. No association was found between DP related MG and the various autoantibodies tested. Immunogenetic analysis showed that three patients had HLA-DR1, two HLA-DR3, one HLA-DR4 and one HLA-DR5. In conclusion, the clinical presentation of DP-induced MG seems similar to idiopathic MG. DP-related MG is relatively benign, although it sometimes can cause life-threatening muscle weakness requiring aggressive therapy. The relatively small number of patients included in this study, however, does not permit any firm conclusions regarding the HLA associations of DP-related MG.
Modeling of the time-dependency of in vitro drug cytotoxicity and resistance. (1998)

For potential clinical extrapolation of in vitro findings, it is of interest to relate the measured effect of an anticancer agent to concentration and exposure time. The Hill model (A. V. Hill, J. Physiol., 40: iv-vii, 1910) is commonly used to describe pharmacodynamic (PD) effects, including drug-induced growth inhibition of cancer cells in vitro. The IC(X)n x T = k relationship, in which IC(X) is the concentration of agent required to reduce cell growth by X%, T is the exposure time, and n and k are estimable parameters, was first applied to bacterial disinfectant action and then was successfully used to model anticancer drug potency as a function of exposure time (D. J. Adams, Cancer Res., 49: 6615-6620, 1989). Our goal was to create a new global PD modeling paradigm to facilitate the quantitative assessment of the growth-inhibitory effect of anticancer agents as a function of concentration and exposure time. Wild-type human ovarian A2780 and ileocecal HCT-8 carcinoma cells and sublines that were resistant to cisplatin (A2780/CP3), doxorubicin (A2780/DX5B), and raltitrexed (RTX) (HCT-8/DW2) were exposed to various anticancer agents, cisplatin, doxorubicin, paclitaxel, trimetrexate, RTX, methotrexate, and AG2034, for periods ranging from 1 to 96 h. Cell growth inhibition was measured with the sulforhodamine B protein dye assay. Patterns of time-dependency of drug potency, slope of the concentration-effect curves, and relative degree of resistance were characterized. Empirical mathematical expressions were built into a global concentration-time-effect model. The global PD model was then fit to the concentration-time-effect data with iteratively reweighted nonlinear regression. Under specific treatment conditions, the examination of the slope and the shape of the concentration-effect curves revealed a large heterogeneity in drug response, e.g., shallow concentration-effect curve or double or triple Hill "roller coaster" concentration-effect curve. These patterns, which were observed at intermediate exposure times in parental and resistant cells for paclitaxel and trimetrexate or only in resistant HCT-8/DW2 cells for RTX, methotrexate, and AG2034, revealed mechanistic insights for the former cases but possible methodological artifacts for the latter cases. The comprehensive PD modeling of the cytotoxic effect of anticancer agents showed that it was possible to modulate drug effect, response heterogeneity, and drug resistance by altering the time of exposure to the agents. This approach will be useful for: (a) describing complex concentration-time-effect surfaces; (b) refining biological interpretations of data; (c) providing insights on mechanisms of drug action and resistance; and (d) generating leads for clinical use of anticancer drugs.
Severity of atopic disease inversely correlates with intestinal microbiota diversity and butyrate-producing bacteria (2014)

The reports on atopic diseases and microbiota in early childhood remain contradictory, and both decreased and increased microbiota diversity have been associated with atopic eczema. In this study, the intestinal microbiota signatures associated with the severity of eczema in 6-month-old infants were characterized. Further, the changes in intestinal microbiota composition related to the improvement of this disease 3 months later were assessed. The severity of eczema correlated inversely with microbiota diversity (r = -0.54, P = 0.002) and with the abundance of butyrate-producing bacteria (r = -0.52, P = 0.005). During the 3-month follow-up, microbiota diversity increased (P < 0.001) and scoring atopic dermatitis values decreased (P < 0.001) in all infants. This decrease coincided with the increase in bacteria related to butyrate-producing Coprococcus eutactus (r = -0.59, P = 0.02). In conclusion, the high diversity of microbiota and high abundance of butyrate-producing bacteria were associated with milder eczema, thus suggesting they have a role in alleviating symptoms of atopic eczema.
Alignment of distantly related protein structures: algorithm, bound and implications to homology modeling (2011)

Supplementary data are available at Bioinformatics online.
Multidrug Resistance Protein 4 Protects Bone Marrow, Thymus, Spleen, and Intestine from Nucleotide Analogue–Induced Damage (2007)

Nucleoside-based analogues are mainstays in the treatment of cancer, viral infections, and inflammatory diseases. Recent studies showing that the ATP-binding cassette transporter, multidrug resistance protein 4, is able to efflux nucleoside and nucleotide analogues from transfected cells suggests that the pump may affect the efficacy of this class of agents. However, the in vivo pharmacologic functions of the pump are largely unexplored. Here, using Mrp4(-/-) mice as a model system, and the nucleotide analogue, 9'-(2'-phosphonylmethoxyethyl)-adenine (PMEA) as a probe, we investigate the ability of Mrp4 to function in vivo as an endogenous resistance factor. In the absence of alterations in plasma PMEA levels, Mrp4-null mice treated with PMEA exhibit increased lethality associated with marked toxicity in several tissues. Affected tissues include the bone marrow, spleen, thymus, and gastrointestinal tract. In addition, PMEA penetration into the brain is increased in Mrp4(-/-) mice. These findings indicate that Mrp4 is an endogenous resistance factor, and that the pump may be a component of the blood-brain barrier for nucleoside-based analogues. This is the first demonstration that an ATP-binding cassette transporter can affect in vivo tissue sensitivity towards this class of agents.
RF Power Amplifier Linearization Method Based on Quadrature Nonlinear Model (2009)

In the predistortion power amplifier linearization system, output of the power amplifier must be feedback to acquire the nonlinear distortion information. After quadrature demodulation, usually both the in-phase and quadrature part of the feedback complex signal should be sampled. This paper proposed a novel predistortion linearization method based on the quadrature nonlinear model, which needs only the in-phase or quadrature part of the feedback complex signal, so the hardware costs can be reduced. Simulation results show the effectiveness of this method for suppressing the spectrum regrowth caused by the nonlinearity of the power amplifier.
Insulin-like growth factor binding protein-related protein 1 (IGFBP-rP1) is a potential tumor suppressor protein for prostate cancer. (1999)

Insulin-like growth factor binding protein-related protein-1 (IGFBP-rP1) has been shown to have decreased expression in the progression from benign to malignant prostate epithelial cells (V. Hwa et al., J. Clin Endocrinol. Metab., 83: 4355-4362, 1998). The present study was undertaken to determine the effects of the re-expression of IGFBP-rP1 in a cell line from a model of human prostate cancer, M12, in which IGFBP-rP1 expression had been demonstrated to decrease from the parent epithelial cell, P69, to the malignant subline, M12. An IGFBP-rP1 cDNA encoding the protein was transfected into M12 cells in a plasmid that resulted in constitutive-expression of IGFBP-rP1. Clones of transfected M12 cells were selected for low (L) and high (H) levels of expression, and the plasmid vector alone was transfected into M12 as a control. After transfection, there was a marked alteration in the morphology of the M12 cells such that the H clones had an elongated appearance when compared with the M12 control cells. The M12 clones overexpressing IGFBP-rP1 had a dose-related increase in population doubling time, decreased colony formation in soft agar, an increased propensity to undergo apoptosis in response to 6-hydroxyurea, and decreased tumor formation in male athymic, nude mice. These data suggest that IGFBP-rP1 may have a suppressive effect on prostate cancer development.
Galectins, galactoside-binding mammalian lectins: clinical application of multi-functional proteins. (2001)

Galectins are beta-galactoside binding mammalian lectins and they share homologous carbohydrate recognition domains. To date, 11 members of galectin family have been cloned and identified. They have been shown to play roles in diverse biological events, such as embryogenesis, oncogenesis, adhesion and proliferation of the cells, receptor for advanced glycation end products, mRNA splicing, bacterial colonization, apoptosis, and in the modulation of the immune response. The mechanisms by which galectins exert these diverse effects remain largely unknown. However, the elucidation of multi-functional proteins belong to galectin family are going to open new fields in clinical science including diagnosis and therapy of autoimmune disorders, cancers, and vascular complications in diabetes and hypertension.&#60;/P&#62;
PEG-ADA: An alternative to haploidentical bone marrow transplantation and an adjunct to gene therapy for adenosine deaminase deficiency (1995)

PEG-ADA is a long-circulating form of adenosine deaminase (ADA) that has been in use for > 8 years as replacement therapy for severe combined immunodeficiency disease due to ADA deficiency. Treatment with PEG-ADA almost completely corrects metabolic abnormalities, allowing the recovery of a variable degree of immune function. Although not normal, the level of function achieved has in most cases been sufficient to protect against opportunistic and life-threatening infections. PEG-ADA has been used as an alternative for patients who lack an HLA-identical bone marrow donor, but are judged to be at too high a risk for undergoing HLA-haploidentical marrow transplantation. To date, mortality and morbidity with PEG-ADA have been less than for the latter procedure. PEG-ADA has also been an important adjunct to attempts to develop somatic cell gene therapy for ADA deficiency, although its continued use poses a problem for evaluation of the benefit of gene therapy. As a true "orphan drug" developed to treat a very small patient population, the cost per patient of PEG-ADA is very high.
Stress analysis of shallow trench isolation for 256 M DRAM and beyond (2002)

The stress generation of the shallow trench isolation has been systematically investigated using the stress simulation and the experiment. It is found that the scale-down of the isolation pitch causes a remarkable stress generation due to the overlap of the stress from both trench sides. Therefore a small isolation pitch causes the crystal defects generation with ease. We carried out the stress analysis against the various process parameters in detail. The high temperature sacrificial oxidation can effectively eliminate the stress generation. It was confirmed that enough isolation characteristics can maintain up to 0.1 /spl mu/m regime to give a careful consideration of the stress reduction.
Voltage scheduling in the IpARM microprocessor system (2000)

Microprocessors represent a significant portion of the energy con?sumed in portable electronic devices. Dynamic Voltage Scaling (DVS) allows a device to reduce energy consumption by lowering its processor speed at run-time, allowing a corresponding reduction in processor voltage and energy. A voltage scheduler determines the appropriate operating voltage by analyzing application con?straints and requirements. A complete software implementation, including both applications and the underlying operating system, shows that DVS is effective at reducing the energy consumed with?out requiring extensive software modification.
PNA−Nitrogen Mustard Conjugates Are Effective Suppressors of HER-2/neu and Biological Tools for Recognition of PNA/DNA Interactions (2006)

Peptide nucleic acids (PNAs) are promising tools for gene regulation. One of the challenges of using PNAs as gene regulators is the need to optimize the efficiency of interaction with critical sequences of DNA. To improve the efficiency of binding between PNAs and the HER-2/neu promoter, mono- and bis-pyrimidine-rich PNAs were conjugated to a nitrogen mustard at either the amino or carboxy terminus. Gel shift analysis demonstrated that conjugation to an alkylating agent slowed PNA binding and favored PNA:DNA:DNA triplex helix formation while preserving a high binding affinity. Sites of DNA alkylation were visualized by piperidine cleavage and showed PNA binding first by Hoogsteen bond formation with the target duplex to form a stable PNA:DNA:DNA triplex structure which is later converted to a PNA:DNA:PNA triple helix by strand invasion and Watson-Crick base pairing by a second PNA molecule. In this way, PNA-directed DNA alkylation was used to deduce the mode of PNA binding. Transient transfection experiments demonstrated that the PNA-nitrogen mustard conjugates suppressed HER-2/neu expression by up to 80%. In comparison with an unmodified mono-PNA or a bis-PNA, these results indicate that the covalent adducts stabilized PNA binding in cells and suggest that the conjugation of PNAs to nitrogen mustards is a robust strategy for developing antigene PNA oligonucleotides to prevent transcription.
Comparative analysis of approximate blocking techniques for entity resolution (2016)

Entity Resolution is a core task for merging data collections. Due to its quadratic complexity, it typically scales to large volumes of data through blocking: similar entities are clustered into blocks and pair-wise comparisons are executed only between co-occurring entities, at the cost of some missed matches. There are numerous blocking methods, and the aim of this work is to offer a comprehensive empirical survey, extending the dimensions of comparison beyond what is commonly available in the literature. We consider 17 state-of-the-art blocking methods and use 6 popular real datasets to examine the robustness of their internal configurations and their relative balance between effectiveness and time efficiency. We also investigate their scalability over a corpus of 7 established synthetic datasets that range from 10,000 to 2 million entities.