gebhart/patrepeval huggingface dataset:
IL-5 Production by NK Cells Contributes to Eosinophil Infiltration in a Mouse Model of Allergic Inflammation (1998)

IL-5 production in vivo plays a unique role in the production, activation, and localization of eosinophils in a variety of allergic conditions. The current paradigm suggests that allergen-specific Th2 cells are the main source for the IL-5 production. The experiments outlined in this work, however, suggest that in vivo production of IL-5 by NK cells can separately influence eosinophil-associated inflammatory responses. Specifically, a mouse model of allergic inflammation was used in which C57BL/6 mice were immunized and challenged with a short ragweed Ag extract, known to induce a selective eosinophilia within the peritoneal cavity. Peritoneal lavage fluids from these mice also contained increased numbers of T cells and NK cells, as well as significantly elevated levels of IL-4, IL-5, and IFN-gamma. Flow-cytometric analysis of cytokine-producing cells in peritoneal lavage fluid revealed increased numbers of IL-5-producing cells in both T cell and NK cell populations following allergen exposure. Depletion of NK cells by treatment with NK1.1 Abs selectively reduced the number of infiltrating eosinophils by more than 50%. Moreover, the inhibition of the infiltration of eosinophils was accompanied by a complete loss of IL-5-producing NK cells and significantly reduced levels of peritoneal lavage fluid IL-5, whereas the number of IL-5-producing T cells was not affected. Thus, the results presented in this study provide clear evidence for a novel immunoregulatory function of NK cells in vivo, promoting allergen-induced eosinophilic inflammatory responses by the production of IL-5.
Synthesis of 1,2,3,4-tetrahydro-.BETA.-carboline derivatives as hepatoprotective agents. III. Introduction of substituents onto methyl 1,2,3,4-tetrahydro-.BETA.-carboline-2-carbodithioate. (1987)

Dithiocarbamates of various substituted tetrahydro-β-carbolines were synthesized and tested for hepatoprotective activity against carbon tetrachloride (CCl4) -induced liver damage in mice. Structure-activity relationships were investigated. Some neighboring group participation of the 3-substituent with the dithiocarbamate group appeared to be important for the manifestation of activity. The compounds (1a, 2a, and 3i) with hydrophilic substituents at the 3 poisition exhibited significant activity. Substitution at the 9 position of the 3-carboxylic acid (1a) lowered the activity.
One of the CD3ε Subunits within a T Cell Receptor Complex Lies in Close Proximity to the Cβ FG Loop (1998)

A recent crystal structure of the N15 alpha/beta-T cell receptor (TCR) in complex with an Fab derived from the H57 Cbeta-specific monoclonal antibody (mAb) shows the mAb fragment interacting with the elongated FG loop of the Cbeta domain. This loop creates one side wall of a cavity within the TCR Ti-alpha/beta constant region module (CalphaCbeta) while the CD and EF loops of the Calpha domain form another wall. The cavity size is sufficient to accommodate a single nonglycosylated Ig domain such as the CD3epsilon ectodomain. By using specific mAbs to mouse TCR-beta (H57) and CD3epsilon (2C11) subunits, we herein provide evidence that only one of the two CD3epsilon chains within the TCR complex is located in close proximity to the TCR Cbeta FG loop, in support of the above notion. Moreover, analysis of T cells isolated from transgenic mice expressing both human and mouse CD3epsilon genes shows that the heterologous human CD3epsilon component can replace the mouse CD3epsilon at this site. The location of one CD3epsilon subunit within the rigid constant domain module has implications for the mechanism of signal transduction throughout T cell development.
Regional heparinization via simultaneous separation and reaction in a novel Taylor-Couette flow device (1999)

The development of a safe and efficient bioreactor design has remained a challenge for the clinical application of immobilized enzymes. Specifically, the use of immobilized heparinase I has been the target of many studies to make heparin anticoagulation therapy safer for the critically ill patient with kidney failure or heart disease. We have investigated the use of Taylor-Couette flow for a novel type of bioreactor. In a previous study, we showed that the fluidization of agarose immobilized heparinase within Taylor vortices in whole blood can lead to extensive blood damage in the form of cell depletion and hemolysis. Based on these findings, we designed and developed a reactor, referred to as vortex-flow plasmapheretic reactor (VFPR), that incorporated plasmapheresis and fluidization of the agarose in the reactive compartment, separate from the whole-blood path. In the present study, immobilized heparinase I was tested as a means of achieving regional heparinization of a closed circuit. This is a method in which heparin is infused into the extracorporeal circuit predialyzer and neutralized postdialyzer. Saline studies were performed with an immobilized heparinase I-packed bed and with the VFPR. An in vitro feasibility study was performed with the VFPR using human blood. The VFPR achieved heparin conversions of 44 +/- 0.5% and 34 +/- 2% in saline and blood, respectively. In addition, the VFPR caused no blood damage. We report a novel method to achieve fluidization which depended on secondary, circumferencial flow, and was independent of the primary flow through the device.
Optimal control of circuit quantum electrodynamics in one and two dimensions (2010)

Optimal control can be used to significantly improve multi-qubit gates in quantum information processing hardware architectures based on superconducting circuit quantum electrodynamics. We apply this approach not only to dispersive gates of two qubits inside a cavity, but, more generally, to architectures based on two-dimensional (2D) arrays of cavities and qubits. For high-fidelity gate operations, simultaneous evolutions of controls and couplings in the two coupling dimensions of cavity grids are shown to be significantly faster than conventional sequential implementations. Even under experimentally realistic conditions speedups by a factor of three can be gained. The methods immediately scale to large grids and indirect gates between arbitrary pairs of qubits on the grid. They are anticipated to be paradigmatic for 2D arrays and lattices of controllable qubits.
Dual role for TWEAK in angiogenic regulation (2002)

Angiogenic regulators modulate endothelial cell functions, including proliferation, migration, secretion, and adhesion, through their action on endothelial cells or other cell types. TWEAK, a novel member of the tumor necrosis factor family, appears to be a pro-angiogenic agent on the basis of previous studies demonstrating its ability to induce interleukin-8 production by epithelial tumor lines, stimulate proliferation of human vascular cell types and neovascularization in rat corneas. Here, we further characterized the angiogenic potential of TWEAK, revealing a dual role for TWEAK as an angiogenic regulator. We demonstrate that TWEAK is a potent inducer of endothelial cell survival and cooperates with basic fibroblast growth factor to induce the proliferation and migration of human endothelial cells and morphogenesis of capillary lumens. In contrast, TWEAK antagonizes the morphogenic response of endothelial cells to vascular endothelial growth factor (VEGF) without inhibiting VEGF-induced survival or proliferation. Thus, our observations suggest that TWEAK may differentially regulate microvascular growth, remodeling and/or maintenance in vivo, depending upon the angiogenic context.
Exciton-controlled magnetization in single magnetic quantum dots (2005)

We report on low temperature polarization-resolved imaging of single magnetic self-assembled CdMnTe quantum dots (QDs) in the absence of magnetic field. Using longitudinal optical phonon-assisted absorption to photoexcite spin-polarized excitons into a QD ground state, we find that the magnetic impurities within CdMnTe QDs can be aligned ferromagnetically with a single emission lines exhibiting a circular polarization as large as 65%. These results demonstrate that the magnetization of a single magnetic QD can be optically controlled with a suitably polarized laser.
Flt3 ligand stimulates proliferation and inhibits apoptosis of acute myeloid leukemia cells: regulation of Bcl-2 and Bax (1996)

Flt3/flk-2 ligand (flt3-L) is a potent costimulator of normal bone marrow (BM) myeloid progenitors. Flt3-L is produced by BM stromal cells and its receptor is expressed in the majority of acute myeloid leukemia (AML) cases. Therefore, flt3-L may play a role in the paracrine and/or autocrine loops sustaining leukemic cell growth. We evaluated the effects of recombinant human flt3-L on proliferation, apoptosis, and Bcl-2 and Bax expression in primary AML cells and compared them with those of stem cell factor (SCF). Mononuclear BM cells from patients with newly diagnosed AML were cultured in serum-free conditions with flt3-L, SCF, granulocyte colony-stimulating factor (G-CSF) and granulocyte macrophage-colony-stimulating factor (GM-CSF) alone and in combination. In 9 of 10 samples, flt3-L significantly increased [3H]thymidine uptake (geometric mean stimulation index, 7.5; range, 2.4 to 41.5). Flt3-L also increased the number of AML blast colonies by 126% (range, 61% to 181%). In these 9 samples, flt3-L significantly enhanced the proliferative response triggered by G-CSF or GM-CSF. Flt3-L prevented apoptosis in AML blasts. It reduced the number of apoptotic cells by 36% +/- 3.9% compared with control cultures. Combining flt3-L with G-CSF or GM-CSF doubled the antiapoptotic effect. Cellular Bcl-2 and Bax levels were determined separately for apoptotic and nonapoptotic cells by flow cytometry. Cells undergoing spontaneous apoptosis had low Bcl-2 and high Bax levels, whereas nonapoptotic cells had high Bcl-2 and low Bax levels. Flt3-L alone or in combination with G-CSF or GM-CSF did not upregulate Bcl-2. However, Bax expression decreased in viable cells in the presence of these cytokines and the lowest level was achieved when a combination of flt3 and GM-CSF was used. Proliferative and viability effects of flt3-L were similar to those of SCF. Our results demonstrate that flt3-L acts as a stimulatory factor for primary AML cells. The antiapoptotic effects of flt3-L or its combinations with G-CSF or GM-CSF correlate with their ability to prevent upregulation of Bax.
Human CD8+ CTL Specific for the Mycobacterial Major Secreted Antigen 85A (2000)

The role of CD8(+) CTL in protection against tuberculosis in human disease is unclear. In this study, we stimulated the peripheral blood mononuclear cells of bacillus Calmette-Guérin (BCG)-vaccinated individuals with live Mycobacterium bovis BCG bacilli to establish short-term cell lines and then purified the CD8(+) T cells. A highly sensitive enzyme-linked immunospot (ELISPOT) assay for single cell IFN-gamma release was used to screen CD8(+) T cells with overlapping peptides spanning the mycobacterial major secreted protein, Ag85A. Three peptides consistently induced a high frequency of IFN-gamma responsive CD8(+) T cells, and two HLA-A*0201 binding motifs, P(48-56) and P(242-250), were revealed within the core sequences. CD8(+) T cells responding to the 9-mer epitopes were visualized within fresh blood by ELISPOT using free peptide or by binding of HLA-A*0201 tetrameric complexes. The class I-restricted CD8(+) T cells were potent CTL effector cells that efficiently lysed an HLA-A2-matched monocyte cell line pulsed with peptide as well as autologous macrophages infected with Mycobacterium tuberculosis or recombinant vaccinia virus expressing the whole Ag85A protein. Tetramer assays revealed a 6-fold higher frequency of peptide-specific T cells than IFN-gamma ELISPOT assays, indicating functional heterogeneity within the CD8(+) T cell population. These results demonstrate a previously unrecognized, MHC class I-restricted, CD8(+) CTL response to a major secreted Ag of mycobacteria and supports the use of Ag85A as a candidate vaccine against tuberculosis.
Controlling the Aspect Ratio of Inorganic Nanorods and Nanowires (2002)

Semiconductors and metals exhibit unusual optical, electronic, and magnetic properties on the nanometer scale. Chemists and materials scientists are developing methods to make non-spherical shapes of semiconductors and metals on the nanometer scale. We use a seed-mediated growth approach to make metallic nanorods and nanowires in homogeneous solution. Control of the ratio of metallic spherical seeds to metal salt in the reduction reaction contyrols the aspect ratio of the resulting rods and wires.
On the Antimicrobial Activity and Syntheses of Carbanilide and Salicylanilide Derivatives (1982)

Amino compounds of diphenyl ether (or sulfide) and naphthyl ether were condensed with 2, 4-(or 3, 4-) dichlorophenyl isocyanate in benzene to form their carbanilides (1-25). Amino compounds of naphthyl ether were thiocyanated with ammonium thiocyanate and bromine in acetic acid to form their thiocyanato compounds (26-29). Amino compounds of naphthyl ether and diphenylamine (or sulfide) were condensed with salicylic acid or 5-chlorosalicylic acid using phosphorus trichloride in xylene to form their salicylanilide (30-37). Antimicrobial tests of the synthesized compounds showed that carbanilides (10, 12, 13, 20, 21) had a strong antimicrobial activity against Staphylococcus aureus.
Estrogen Receptor-β-selective Ligands Alleviate High-fat Diet- and Ovariectomy-induced Obesity in Mice (2010)

Obesity is an epidemic problem affecting millions of people in the Western hemisphere and costs the United States economy more than $200 billion annually. Currently, there are no effective treatments to combat obesity. Recent studies have implicated the constitutive activity of estrogen receptor (ER) β as an important regulator of metabolic diseases. However, the potential of ER-β-selective ligands to offset obesity is not clear. We evaluated the pharmacological effect of ER-β-selective ligands (β-LGNDs) in animal models of high-fat diet- and ovariectomy-induced obesity. Ligand binding, transactivation, and uterotrophic studies with β-LGNDs demonstrated selectivity for ER-β over ER-α. Animals fed a high-fat diet showed a significant increase in body weight, and this weight gain was attenuated by β-LGNDs. High-fat diet-mediated increases in serum cholesterol, leptin, glucose, and fat accumulation in organs were also reduced by β-LGNDs. In addition, MRI scanning indicated that β-LGNDs altered body composition by reducing fat mass and increasing lean body mass. Organ weights and gene expression analyses demonstrated that adipose tissue is the center of action for β-LGNDs, and the reduction in body weight is likely due to increased energy expenditure. In vitro and in vivo mechanistic studies indicated that the anti-obesity effects of β-LGNDs were due to indirect peroxisome proliferator-activated receptor γ antagonistic actions requiring the ligand binding domain of ER-β and through abrogation of the ability of PGC-1 to coactivate peroxisome proliferator-activated receptor γ. In conclusion, these studies indicate that ligand-activated ER-β is a potential therapeutic target to combat obesity and obesity-related metabolic diseases.
Object scene flow for autonomous vehicles (2015)

This paper proposes a novel model and dataset for 3D scene flow estimation with an application to autonomous driving. Taking advantage of the fact that outdoor scenes often decompose into a small number of independently moving objects, we represent each element in the scene by its rigid motion parameters and each superpixel by a 3D plane as well as an index to the corresponding object. This minimal representation increases robustness and leads to a discrete-continuous CRF where the data term decomposes into pairwise potentials between superpixels and objects. Moreover, our model intrinsically segments the scene into its constituting dynamic components. We demonstrate the performance of our model on existing benchmarks as well as a novel realistic dataset with scene flow ground truth. We obtain this dataset by annotating 400 dynamic scenes from the KITTI raw data collection using detailed 3D CAD models for all vehicles in motion. Our experiments also reveal novel challenges which cannot be handled by existing methods.
CRISPR guide RNA design for research applications (2016)

The rapid rise of CRISPR as a technology for genome engineering and related research applications has created a need for algorithms and associated online tools that facilitate design of on-target and effective guide RNAs (gRNAs). Here, we review the state of the art in CRISPR gRNA design for research applications of the CRISPR-Cas9 system, including knockout, activation, and inhibition. Notably, achieving good gRNA design is not solely dependent on innovations in CRISPR technology. Good design and design tools also rely on availability of high-quality genome sequence and gene annotations, as well as on availability of accumulated data regarding off-targets and effectiveness metrics.
Isolation Kernel and Its Effect on SVM (2018)

This paper investigates data dependent kernels that are derived directly from data. This has been an outstanding issue for about two decades which hampered the development of kernel-based methods. We introduce Isolation Kernel which is solely dependent on data distribution, requiring neither class information nor explicit learning to be a classifier. In contrast, existing data dependent kernels rely heavily on class information and explicit learning to produce a classifier. We show that Isolation Kernel approximates well to a data independent kernel function called Laplacian kernel under uniform density distribution. With this revelation, Isolation Kernel can be viewed as a data dependent kernel that adapts a data independent kernel to the structure of a dataset. We also provide a reason why the proposed new data dependent kernel enables SVM (which employs a kernel through other means) to improve its predictive accuracy. The key differences between Random Forest kernel and Isolation Kernel are discussed to examine the reasons why the latter is a more successful tree-based kernel.
A working anti-taping system for cable pay-per-view (1989)

An antitaping system for cable pay-per-view services that utilizes the timing and servo control differences between a TV and VCR is described. This system allows movies or event programming to be shown on a television set but be rendered unrecordable by video tape recording devices. Attention is given to the system theory, the hardware design, the distribution configuration of the system, and its field testing.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Germline polymorphisms of RET and GFRA1 genes in patients with medullary thyroid carcinoma (2006)

The association of RET and GFRA1 polymorphisms with a predisposition to sporadic medullary thyroid cancer (MTC) and their effects on the clinical features of hereditary and sporadic MTC were studied in 67 MTC patients (22 hereditary and 45 sporadic), 3 asymptomatic carriers of mutant RET, and 178 healthy control residents of Russia. RET exons 8, 10, 11, 13, 14, 15, and 16 and intron 1 along with the GFRA1 5′-UTR were screened by PCR and subsequent direct sequencing or RFLP analysis. Eight polymorphic variants of RET (exons 11, 13, 14, and 15 and introns 1, 8, 13, and 14) and four GFRA1 polymorphisms were detected. Linkage disequilibrium was found between RET variants G691S and S904S, L769L and IVS8, and S836S and IVS13. In sporadic MTC the allele frequency of only one polymorphic RET variant, L769L, was significantly lower than in the control group. In hereditary MTC a significant overrepresentation of the S836S and underrepresentation of the S904S polymorphic variants were observed as compared to groups with sporadic MTC and the controls. Cosegregation was not found between individual polymorphisms and the phenotype of sporadic MTC. In patients with hereditary MTC whose genotype had the polymorphic L769L and the wild-type S836S variants, the disease manifested 20 years later, on average, than in individuals with polymorphic L769L and S836S or with wild-type L769L (P = 0.01). The results suggest a protective role of the L769L polymorphism in sporadic MTC and a modulating effect of the combination polymorphic L769L with wild-type S836S on the clinical outcome of hereditary MTC.
Probe design and chemical sensing (1994)

Emerging Biomedical Applications of Timeresolved Fluorescence Spectroscopy J.R. Lakowicz. Principles of Fluorescent Probe Design for Ion Recognition B. Valeur. Fluorescence Chemosensors for Cations, Anions, and Neutral Analytes A.W. Czarnik. Design and Applications of Highly Luminescent Transition Metal Complexes J.N. Demas, B.A. DeGraff. Fluorescence Probes Based on Twisted Intramolecular Charge Transfer TICT States and other Adiabatic Photoreactions W. Rettig, R. Lapouyade. Red and Nearinfrared Fluorometry R.B. Thompson. Nearinfrared Fluorescence Probes G.A. Casay, et al. Fluorescence Spectroscopy in Turbid Media and Tissues D. Oelkrug. Real Time Chemical Sensing Employing Luminescence Techniques J.R. Alcala. Lifetimebased Sensing H. Szmacinski, J.R. Lakowicz. Fiber Optic Fluorescence Thermometry K.T.V. Grattan, Z.Y. Zhang. Instrumentation for Red/Near Infrared Fluorescence D.J.S. Birch, G. Hungerford. Application of Fluorescence Sensing to Bioreactors G. Rao, et al. Principles of Fluorescence Immunoassay A. Ozinskas. Index.
Statistical validation of intermediate endpoints for chronic diseases (1992)

We discuss the implementation of a criterion due to Prentice for the statistical validation of intermediate endpoints for chronic disease. The criterion involves examining in a cohort or intervention study whether an exposure or intervention effect, adjusted for the intermediate endpoint, is reduced to zero. For example, to examine whether serum cholesterol level is an intermediate endpoint for coronary heart disease (CHD), we may investigate the effect of the cholesterol lowering drug cholestyramine on CHD incidence adjusted for serum cholesterol levels. We show that use of this criterion will usually demand some form of model selection. When the unadjusted exposure or treatment effect is less than four times its standard error, the analysis can usually lead only to a weak form of validation, a conclusion that the data are not inconsistent with the validation criterion. More significant unadjusted exposure effects offer the potential for stronger types of validation statement such as 'the intermediate endpoint explains at least 50 per cent (or 75 per cent) of the exposure effect'.
Olanzapine versus placebo for out-patients with anorexia nervosa (2011)

This small study suggests that olanzapine is generally well tolerated by, and may provide more benefit than placebo for out-patients with AN. Further study is indicated to determine whether olanzapine may affect psychological symptoms in addition to BMI.
Human papillomavirus DNA sequences in adenocarcinoma of the uterine cervix in Indian women (1993)

HPV 16 is the type present almost exclusively in squamous cell carcinoma of Indian women. A higher frequency of HPV 16 in adenocarcinoma of Indian women, in contrast to HPV 18, as reported from other regions, may be attributed to geographic variation rather than to histologic differences only, and both HPV 16 and 18 may be present in adenocarcinoma of the uterine cervix.
Impaired production of Th1 cytokines and increased frequency of Th2 subsets in PBMC from advanced cancer patients. (1999)

These results indicated that an imbalance of Th1 and Th2 was found not only in the frequency of the subsets in PBMC, but also in the capacity for cytokine-production.