gebhart/patrepeval huggingface dataset:
NF-κB Signaling Promotes Both Cell Survival and Neurite Process Formation in Nerve Growth Factor-Stimulated PC12 Cells (2000)

Nerve growth factor binds to the TrkA and p75(NTR) (p75) and generates signals leading to neuronal cell survival, differentiation, and programmed cell death. Here we describe a series of experiments involving selective activation of either TrkA or p75 in which distinct cell-signaling intermediates promote different cellular consequences. We analyzed pheochromocytoma 12 (PC12) cells stably expressing chimeras consisting of the extracellular domain of PDGF receptor (PDGFR) fused to the transmembrane and cytoplasmic segments of p75 or TrkA. Because PC12 cells lack endogenous PDGFR, addition of PDGF to these cell lines permits selective activation of the p75 or TrkA responses without stimulating endogenous receptors. Although both p75 and TrkA activated nuclear factor-kappaB (NF-kappaB), we show that distinct proximal-signaling intermediates are used by each receptor. A dominant-negative mutant of TRAF6 blocked p75- but not TrkA-mediated induction of NF-kappaB. Conversely a dominant-negative mutant of Shc inhibited TrkA but not p75 activation of NF-kappaB. Both of these distinct signaling pathways subsequently converge, leading to activation of the IkappaB kinase complex. Moreover, the activation of NF-kappaB by these distinct pathways after stimulation of either TrkA or p75 leads to different physiological consequences. Blocking p75-mediated activation of NF-kappaB by ecdysone-inducible expression of a nondegradable mutant of IkappaBalpha significantly enhanced apoptosis. In contrast, blocking NF-kappaB induction via TrkA significantly inhibited neurite process formation in PC12 cells. Together these findings indicate that, although both of these receptors lead to the activation of NF-kappaB, they proceed via distinct proximal-signaling intermediates and contribute to different cellular outcomes.
Single-cell epigenomics: powerful new methods for understanding gene regulation and cell identity (2016)

Emerging single-cell epigenomic methods are being developed with the exciting potential to transform our knowledge of gene regulation. Here we review available techniques and future possibilities, arguing that the full potential of single-cell epigenetic studies will be realized through parallel profiling of genomic, transcriptional, and epigenetic information.
Cholesterol is essential for macrophage inflammatory protein 1β binding and conformational integrity of CC chemokine receptor 5 (2002)

The chemokine receptor, CCR5, is used as a human immunodeficiency virus coreceptor in combination with CD4 during transmission and early infection. CCR5 has been shown to be palmitoylated and targeted to cholesterol- and sphingolipid-rich membrane microdomains termed "lipid rafts." However, the role of cholesterol and lipid rafts on chemokine binding and signaling through CCR5 remains unknown. We found that cholesterol extraction by hydroxypropyl-beta-cyclodextrin (BCD) significantly reduced the binding and signaling of macrophage inflammatory protein 1 beta (MIP-1 beta) using CCR5-expressing CEM-NKR T cells. Reloading treated cells with cholesterol but not 4-cholesten-3-one, an oxidized form of cholesterol, restored MIP-1 beta binding to BCD-treated cells. Antibodies specific for distinct CCR5 epitopes lost their ability to bind to the cell surface after cholesterol extraction to varying degrees. Moreover, cells stained with fluorescently labeled MIP-1 beta extensively colocalized with the GM1 lipid raft marker while using anti-CCR5 antibodies; most of CCR5 on these cells only partially colocalized with GM1, suggesting that active ligand binding facilitates receptor association with lipid rafts or that raft association promotes a higher affinity conformation of CCR5. Together, these data demonstrate that cholesterol and lipid rafts are important for the maintenance of the CCR5 conformation and are necessary for both the binding and function of this chemokine receptor.
Fe-Catalyzed C-H Functionalization and Couplingof Alcohols with Alkenes (2009)

A novel iron-catalyzed C(sp³)-C(sp³) coupling between alcohols and mono- or 1,1-di­substituted alkenes is reported. The reaction proceeds via direct C(sp³)-H functionalization of the alcohol. Tertiary alcohols can be used instead of alkenes as substrates.
DNS prefetching and its privacy implications: when good things go bad (2010)

A recent trend in optimizing Internet browsing speed is to optimistically pre-resolve (or prefetch) DNS resolutions. While the practical benefits of doing so are still being debated, this paper attempts to raise awareness that current practices could lead to privacy threats that are ripe for abuse. More specifically, although the adoption of several browser optimizations have already raised security concerns, we examine how prefetching amplifies disclosure attacks to a degree where it is possible to infer the likely search terms issued by clients using a given DNS resolver. The success of these inference attacks relies on the fact that prefetching inserts a significant amount of context into a resolver’s cache, allowing an adversary to glean far more detailed insights than when this feature is turned off. 1
AdaptIS: Adaptive Instance Selection Network (2019)

We present Adaptive Instance Selection network architecture for class-agnostic instance segmentation. Given an input image and a point (x, y), it generates a mask for the object located at (x, y). The network adapts to the input point with a help of AdaIN layers [13], thus producing different masks for different objects on the same image. AdaptIS generates pixel-accurate object masks, therefore it accurately segments objects of complex shape or severely occluded ones. AdaptIS can be easily combined with standard semantic segmentation pipeline to perform panoptic segmentation. To illustrate the idea, we perform experiments on a challenging toy problem with difficult occlusions. Then we extensively evaluate the method on panoptic segmentation benchmarks. We obtain state-of-the-art results on Cityscapes and Mapillary even without pretraining on COCO, and show competitive results on a challenging COCO dataset. The source code of the method and the trained models are available at https://github.com/saicvul/adaptis.
The origin of fibroblasts and mechanism of cardiac fibrosis (2010)

Fibroblasts are at the heart of cardiac function and are the principal determinants of cardiac fibrosis. Nevertheless, cardiac fibroblasts remain poorly characterized in molecular terms. Evidence is evolving that the cardiac fibroblast is a highly heterogenic cell population, and that such heterogeneity is caused by the distinct origins of fibroblasts in the heart. Cardiac fibroblasts can derive either from resident fibroblasts, from endothelial cells via an endothelial-mesenchynmal transition or from bone marrow-derived circulating progenitor cells, monocytes and fibrocytes. Here, we review the function and origin of fibroblasts in cardiac fibrosis.NB. The information given is correct.
Mitochondria and ageing: winning and losing in the numbers game (2007)

Mitochondrial dysfunction has long been considered a key mechanism in the ageing process but surprisingly little attention has been paid to the impact of mitochondrial number or density within cells. Recent reports suggest a positive association between mitochondrial density, energy homeostasis and longevity. However, mitochondrial number also determines the number of sites generating reactive oxygen species (ROS) and we suggest that the links between mitochondrial density and ageing are more complex, potentially acting in both directions. The idea that increased density, especially when combined with mitochondrial dysfunction, might accelerate ageing is supported by a negative correlation between mitochondrial density and maximum longevity in an interspecies comparison in mammals, and by evidence for an intimate interconnection between cellular ROS levels, mitochondrial density and cellular ageing. Recent data suggest that retrograde response, which activates mitochondrial biogenesis, accompanies cellular ageing processes. We hypothesise that increased mitochondrial biogenesis, and possibly also impaired degradation and segregation of mitochondria, if occurring as adaptation to pre-existing mitochondrial dysfunction, might aggravate ROS production and thus actively contribute to ageing.
Effect of tamoxifen on cell lines displaying the multidrug-resistant phenotype [see comments] (1991)

Abstract We examined the effect of tamoxifen (Tmx), verapamil, and daunorubicin (DNR) in two cell lines that displayed the multidrug-resistant (MDR) phenotype and used laser flow cytometry to quantitate intracellular DNR content. In the vinblastine-resistant human lymphoblastic lymphoma cell line CEM-VBL, simultaneous incubation of DNR with Tmx 10 mumol/L or Tmx 50 mumol/L increased intracellular DNR fluorescence in a dose-dependent manner and demonstrated an uptake pattern similar to that seen with DNR and verapamil. Similar results were obtained in the vincristine- resistant human myeloid leukemia cell line HL-60/RV+. Cellular retention of DNR was also measured in both cell lines and results suggested that continuous exposure of the cells to Tmx resulted in higher intracellular DNR content compared with cells resuspended in fresh medium. No effect of Tmx or verapamil was observed in the drug- sensitive parent cell lines CEM or HL-60. Clonogenic experiments were then performed to determine whether Tmx was itself inhibitory to cell growth or whether Tmx potentiated DNR cytotoxicity. Tmx 10 mumol/L did not significantly inhibit either CEM-VBL or HL-60/RV+ cells after a 3- hour exposure followed by culture in methylcellulose. Tmx 50 mumol/L was significantly more inhibitory in both cell lines. However, cells that had been incubated with DNR and Tmx 10 mumol/L demonstrated a marked increment in growth inhibition compared with cells that had been incubated with DNR alone or Tmx 10 mumol/L alone. Based on the data presented here, we suggest that clinical testing of Tmx and DNR be pursued in the setting where MDR may play a role.
High-specific-activity 111In-labeled anticarcinoembryonic antigen monoclonal antibody: improved method for the synthesis of diethylenetriaminepentaacetic acid conjugates. (1985)

A new method has been developed for conjugating diethylenetriaminepentaacetic acid (DTPA) to proteins using the N-hydroxysuccinimide active ester of DTPA. The DTPA-active ester was prepared using diisopropylcarbodiimide in a simple single step synthesis. DTPA-conjugated proteins were prepared by adding the DTPA-active ester reaction mixture to protein solutions (5 mg/ml) buffered at pH 7.0 and purified by Sephadex G-50 chromatography. A monoclonal antibody directed against carcinoembryonic antigen was reacted with four different amounts of the DTPA-active ester. Solid-phase enzyme immunoassay showed that the immunological activity of the antibody conjugate was not altered when the active ester: antibody molar ratio was 36:1 or 72:1; however, it decreased when the ratio was 180:1 or 360:1. The antibody heavy and light chains had slightly decreased electrophoretic mobilities when analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, a result consistent with the covalent attachment of DTPA to the protein. Sephadex G-200 chromatography showed that the native and conjugated antibodies were the same size. When the DTPA-conjugated antibody was incubated with 10, 50, and 100 microCi of 111In/micrograms of protein, specific activities of 9.8, 43.1, and 56.3 microCi/micrograms were obtained. Enzyme immunoassay and radioimmunoassay of the 111In-labeled antibody showed that it retained its full immunological activity. The high specific activity of the 111In-labeled antibody makes it suitable for imaging carcinoembryonic antigen-bearing tumors using low doses of antibody.
MicroRNA‐223 is a key factor in osteoclast differentiation (2007)

MicroRNAs (miRNAs) are a class of noncording RNAs that control gene expression by translational inhibition and messenger RNAs (mRNAs) degradation in plants and animals. Although miRNAs have been implicated in developmental and homeostatic events of vertebrates and invertebrates, the role of miRNAs in bone metabolism has not been explored. Here, we show that microRNA-223 (miR-223) is expressed in RAW264.7 cells, mouse osteoclast precursor cell lines, and plays a critical role in osteoclast differentiation. We constructed miR-223 short interfering RNA (siRNA) or precursor miR-223 (pre-miR-223) overexpression retroviral vectors, and established miR-223 knockdown by siRNA or pre-miR-223 overexpression in stably infected RAW264.7 cells. Tartrate-resistant acid phosphatase (TRAP)-positive multinucleated cells were observed in miR-223 knockdown cells as well as control cells. In contrast, pre-miR-223 overexpression completely blocked TRAP-positive multinucleated cell formation compared with control cells. Apoptotic cells were not observed in this study. Our results indicate that miR-223 plays an essential role during osteoclast differentiation, and miR-223 might be a viable therapeutic target for a range of bone metabolic disorders with excess osteoclast activity.
The small GTPase Rab22 interacts with EEA1 and controls endosomal membrane trafficking (2002)

Rab22a is a small GTPase that is expressed ubiquitously in mammalian tissues and displays the highest sequence homology to Rab5. In BHK-21 cells, overexpression of the wild-type Rab22a caused formation of abnormally large vacuole-like structures containing the early-endosomal antigen EEA1 but not Rab11, a marker of recycling endosomes or the late-endosomal/lysosomal markers LAMP-1 and lyso-bis-phosphatidic acid. In HeLa cells, overexpressed Rab22a was found on smaller EEA1-positive endosomes, but a portion of the protein was also found in the Golgi complex. Using the yeast two-hybrid system and a biochemical pull-down assay, the GTP-bound form of Rab22a was found to interact with the N-terminus of EEA1. In HeLa cells overexpressing Rab22a or its mutants affected in the GTPase cycle, no significant changes were observed in the uptake of Alexa-transferrin. However, the GTPase-deficient Rab22a Q64L mutant caused a redistribution of transferrin-positive endosomes to the leading edges of cells and a fragmentation of the Golgi complex. In BHK cells, the Q64L mutant caused the accumulation of a fluid phase marker, TRITC-dextran, and a lysosomal hydrolase, aspartylglucosaminidase, in abnormal vacuole-like structures that contained both early and late endosome markers. Both the wild-type Rab22a and the Q64L mutant were found to interfere with the degradation of EGF. These results suggest that Rab22a may regulate the dynamic interactions of endosomal compartments and it may be involved in the communication between the biosynthetic and early endocytic pathways.
Chemiluminescent substrates for alkaline phosphatase: application to ultrasensitive enzyme-linked immunoassays and DNA probes. (1989)

Journal Article Chemiluminescent substrates for alkaline phosphatase: application to ultrasensitive enzyme-linked immunoassays and DNA probes. Get access A P Schaap, A P Schaap Dept. of Chem., Wayne State Univ., Detroit, MI 48202 Search for other works by this author on: Oxford Academic Google Scholar H Akhavan, H Akhavan Dept. of Chem., Wayne State Univ., Detroit, MI 48202 Search for other works by this author on: Oxford Academic Google Scholar L J Romano L J Romano Dept. of Chem., Wayne State Univ., Detroit, MI 48202 Search for other works by this author on: Oxford Academic Google Scholar Clinical Chemistry, Volume 35, Issue 9, 1 September 1989, Pages 1863–1864, https://doi.org/10.1093/clinchem/35.9.1863 Published: 01 September 1989
Respiratory effects of lipopolysaccharide-induced inflammatory lung injury in mice (2000)

The pathogenic mechanisms of lipopolysaccharide (LPS)-induced lung injury have not been classified. This study examined the physiological changes after endotoxin inhalation and related those to features of pulmonary inflammation in mice. Pulmonary mechanics, histopathology, and bronchoalveolar lavage fluid (BALF) from BALB/c mice were analysed at different occasions (3, 24, 48 and 72 h) after inhalation of saline or LPS from Escherichia coli (0.3 (L0.3) or 10 mg x mL(-1) (L10)). Mice were sedated, anaesthetized, and ventilated. After chest wall resection static (Est) and dynamic (Edyn) elastances, deltaE (Edyn-Est), resistive (deltaP1) and viscoelastic/inhomogeneous pressures (deltaP2), and deltaP1+deltaP2 (deltaPtot) were obtained by end-inflation occlusion method. Lungs were prepared for histopathology. In parallel groups, tumour necrosis factor (TNF)-alpha, neutrophils, and protein were evaluated in the BALF. L0.3 and L10 showed a time-dependent production of TNF-alpha preceding a massive neutrophil infiltration. In L10 BALF there was an increase in protein level at 24 and 48 h. Est and Edyn increased early in L0.3 (65%, 63%) and L10 (41%, 51%). In L10 deltaE, deltaP2, and deltaPtot showed a gradual rise. At 72 h all groups were similar. L0.3 showed an early increase in cellularity, which returned to normal at 72 h. L10 presented the same pattern with the cell count remaining elevated until 72 h. In conclusion, lipopolysaccharide inhalation led to elastic and viscoelastic pulmonary changes together with tumour necrosis factor-alpha production and neutrophil infiltration in mouse lung.
Acellular Pertussis Vaccines and Complement Killing ofBordetella pertussis (2004)

Antibody-dependent complement killing of Bordetella pertussis after immunization with a three-component acellular pertussis vaccine was characterized. Postimmunization activity was unchanged for about half of the adult vaccine recipients. The responses of the other individuals were complex, with evidence of both beneficial and antagonistic responses occurring, sometimes in the same individual.
Angular spectral approach to reflection of focused beams with oblique incidence in spherical-planar-pair lenses (1991)

The characteristics of the output signal from spherical-planar-pair (SPP) lenses in the ultrasonic microspectrometer (UMSM) are described. The angular spectral approach is used to obtain the mathematical formula of the output signal. Although isotropic specimens are assumed, anisotropic materials can be treated as well with a small modification. A 2-D approximation is introduced to analyze the specular reflection, the Rayleigh critical angular phenomenon, and V (z) of the specular reflection. Numerical calculations are also performed for specimens with copper substrate, steel substrate, and layered structures, by numerically integrating the 2-D formulas of the output signal. It is found that a ray optical treatment is a good approximation of the wave propagation in the SPP lenses. The incident angular dependence of a reflection coefficient can be estimated by tilting the sensor unit.
Simultaneous Determination of Hydrogen, Methane and Carbon Dioxide of Breath Using Gas-Solid Chromatography. (1992)

The analysis of respiratory hydrogen and methane was estimated as a useful index of intestinal fermentation of undigestible carbohydrate. A simultaneous and precious analysis of these gases as well as carbon dioxide was studied. A gas-impermeable multi-laminated film bag metalized by aluminum vapor was fitted to use as a storage bag; its impermeability was verified by measuring the residual rate of hydrogen after 3 months' storage. Hydrogen, methane and carbon dioxide of the breath gas even at 1 ppm could be determined simultaneously by using a gas-solid chromatography installed with a photoionization detector and active carbon column. To observe the genesis of hydrogen and methane after carbohydrate ingestion, pectin, a typical water-soluble dietary fiber, was fed to healthy volunteers. Increasing excretion of pulmonary hydrogen or methane showed the sign of intestinal fermentation as the results of carbohydrate malabsorption.
Heritable retroviral transgenes are highly expressed in chickens. (1991)

This report describes expression of heritable reticuloendotheliosis virus (REV) vector ME111 in 20 independent lines of transgenic chickens. The results are strikingly different from studies of Moloney virus in transgenic mice, where restricted expression of inherited proviruses has led to their use primarily as insertional mutagens rather than general agents for gene transfer. In contrast, the REV ME111 provirus is actively transcribed in a variety of tissues from transgenic chickens, is expressed from transcriptional control elements present in the long terminal repeat of the provirus, and codes for active neomycin phosphotransferase II. The REV vector system as applied to the chicken represents a departure from the long-established paradigm of retroviral transgenes in mice and provides a new approach to the study of avian biology.
Distillation in microchemical systems using capillary forces and segmented flow (2009)

Distillation is a ubiquitous method of separating liquid mixtures based on differences in volatility. Performing such separations in microfluidic systems is difficult because interfacial forces dominate over gravitational forces. We describe distillation in microchemical systems and present an integrated silicon device capable of separating liquid mixtures based on boiling point differences. Microfluidic distillation is realized by establishing vapor-liquid equilibrium during segmented flow. Enriched vapor in equilibrium with liquid is then separated using capillary forces, and thus enabling a single-stage distillation operation. Design criteria for operation of on-chip distillation is set forth, and the working principle demonstrated by separation of binary mixtures of 50 : 50 mol% MeOH-toluene and 50 : 50 mol% DCM-toluene at 70.0 degrees C. Analysis of vapor condensate and liquid exiting a single-stage device gave MeOH mole fractions of 0.22 +/- 0.03 (liquid) and 0.79 +/- 0.06 (vapor). Similarly, DCM mole fractions were estimated to be 0.16 +/- 0.07 (liquid) and 0.63 +/- 0.05 (vapor). These experimental results were consistent with phase equilibrium predictions.
Signal transduction for melatonin in human lymphocytes: involvement of a pertussis toxin-sensitive G protein (1997)

Abstract We analyzed the melatonin signal transduction in human blood lymphocytes. High affinity melatonin receptors were identified by specific binding of 2-[125I]melatonin ([125I]MEL) to human lymphocyte membranes. Scatchard analysis of [125I]MEL binding revealed high affinity receptors, with a dissociation constant (Kd) of 0.45 nM and a binding capacity (Bmax) of 7.8 fmol/mg protein. Specific [125I]MEL binding was reduced markedly by GTP and its nonhydrolyzable analogues guanosine 5’-beta, gamma-imidotriphosphate (Gpp(NH)p) and guanosine 5’-O-(3-triphosphate) (GTP-gamma-S). Gpp(NH)p inhibited in a dose-dependent manner the [125I]MEL specifically bound to human lymphocyte membranes with a half-maximal inhibition (IC50) of 3.5 +/- 0.6 microM Gpp(NH)p. Treatment of human lymphocyte membranes with Gpp(NH)p increased the Kd value (Kd = 1.20 nM). Melatonin inhibited significantly and in a dose-dependent manner forskolin-stimulated cAMP production in intact human lymphocytes. Melatonin was able to stimulate diacylglycerol production in a dose-dependent manner in human lymphocyte membranes. Pertussis toxin treatment inhibited the specific [125I]MEL binding and blocked the ability of melatonin to both inhibit forskolin-stimulated cAMP production and stimulate diacylglycerol production. Pertussis toxin ADP-ribosylation and Western blot experiments demonstrated the protein expression of alpha i1/2, alpha i3/0, and beta gamma complexes of G proteins in human lymphocyte membranes. The results strongly suggest a pertussis toxin-sensitive melatonin signal transduction pathway in human lymphocytes that involves the inhibition of adenylyl cyclase and the stimulation of phospholipase C.