gebhart/patrepeval huggingface dataset:
Hyposmotic Stress Induces Cell Growth Arrest via Proteasome Activation and Cyclin/Cyclin-dependent Kinase Degradation (2002)

Ordered cell cycle progression requires the expression and activation of several cyclins and cyclin-dependent kinases (Cdks). Hyperosmotic stress causes growth arrest possibly via proteasome-mediated degradation of cyclin D1. We studied the effect of hyposmotic conditions on three colonic (Caco2, HRT18, HT29) and two pancreatic (AsPC-1 and PaCa-2) cell lines. Hyposmosis caused reversible cell growth arrest of the five cell lines in a cell cycle-independent fashion, although some cell lines accumulated at the G(1)/S interface. Growth arrest was followed by apoptosis or by formation of multinucleated giant cells, which is consistent with cell cycle catastrophe. Hyposmosis dramatically decreased Cdc2, Cdk2, Cdk4, cyclin B1, and cyclin D3 expression in a time-dependent fashion, in association with an overall decrease in cellular protein synthesis. However, some protein levels remained unaltered, including cyclin E and keratin 8. Selective proteasome inhibition prevented Cdk and cyclin degradation and reversed hyposmotic stress-induced growth arrest, whereas calpain and lysosome enzyme inhibitors had no measurable effect on cell cycle protein degradation. Therefore, hyposmotic stress inhibits cell growth and, depending on the cell type, causes cell cycle catastrophe with or without apoptosis. The growth arrest is due to decreased protein synthesis and proteasome activation, with subsequent degradation of several cyclins and Cdks.
Transgenic mice containing the human erythropoietin receptor gene exhibit correct hematopoietic and neural expression. (1996)

The erythropoietin receptor (EpoR), known for its role in the proliferation and differentiation of erythroid cells, has been detected in nonhematopoietic tissues. We have reported previously that in addition to hematopoietic expression, EpoR is expressed at high levels in embryonic mouse brain and decreased to nondetectable levels by birth. While using transgenic mice to characterize human EpoR expression, we observed that a 15-kb human EpoR transgene (expressed in hematopoietic tissues but at a reduced level) also exhibited in the embryonic brain low levels of expression that persisted through adulthood. To examine further the basis of tissue and developmental specificity of the human EpoR gene, we produced additional transgenic mice using an 80-kb human EpoR genomic fragment isolated from a P1 phagemid human library. We found that this transgene is expressed appropriately in hematopoietic tissues (including yolk sac, fetal liver, adult spleen, and bone marrow) at levels comparable to the endogenous murine EpoR. The 80-kb transgene also provided high-level expression in the embryonic brain that paralleled the levels of the endogenous murine EpoR and was no longer detectable after birth. These data suggest that the high level of embryonic brain expression may be relevant to the human EpoR gene and that the transgenic mouse with an 80-kb fragment is a suitable model for studying the regulation and possible functional importance of human EpoR expression in the developing embryo.
Human eotaxin represents a potent activator of the respiratory burst of human eosinophils (1996)

Increased numbers of eosinophils are found in parasitic infections, autoimmune diseases and allergic diseases such as allergic asthma. They are activated by distinct cytokines and chemokines leading to the immigration in the inflamed tissue and mediate tissue damage by releasing reactive oxygen species. Here, the effect of the recently cloned CC chemokine human eotaxin was investigated for its ability to affect different eosinophil effector functions and compared to the CC chemokines MCP-3 and RANTES. Human eotaxin induced chemotaxis of human eosinophils in a dose-dependent manner. The range of efficacy of the CC chemokines compared to the well-known chemotaxin C5a was eotaxin = RANTES > MCP-3 = C5a. In addition, eotaxin induced rapid and transient actin polymerization, a prerequisite for cell migration, in eosinophils in the same range of efficacy as observed for chemotaxis. To investigate whether eotaxin was able to activate the respiratory burst of eosinophils, release of reactive oxygen species was measured by lucigenin-dependent chemiluminescence. Eotaxin induced production of significantly high amounts of reactive oxygen species at a concentration between 10 ng/ml and 500 ng/ml. Surprisingly, the effect of eotaxin was comparable to the well-known eosinophil activator C5a. The range of efficacy of the CC chemokines compared to C5a in the activation of the respiratory burst was eotaxin = C5a > MCP-3 > RANTES. Production of reactive oxygen species was inhibited by pertussis toxin, staurosporin, genestein and wortmannin. Furthermore, eotaxin induced transient increases in intracellular calcium concentration ([Ca2+]i) in human eosinophils. Therefore, pertussis toxin-sensitive Gi-proteins, protein kinase C, tyrosine kinase, phosphatidylinositol-3-kinase and transient increases in [Ca2+]i are involved in the signal transduction of eosinophils following stimulation with eotaxin. In summary, this study reveals the importance of the CC chemokine eotaxin as a potent activator of the respiratory burst, actin polymerization and chemotaxis. Eotaxin, therefore, plays an important role not only by attracting eosinophils to the site of inflammation but also by damaging tissue by its capacity to induce the release of reactive oxygen species.
TRPV1 Antagonists as a Potential Treatment for Hyperalgesia (2006)

The vanilloid receptor (TRPV1) is a member of the transient receptor potential family of ion channels that is highly expressed in nociceptive primary afferent sensory neurons. TRPV1 is a voltage-dependent cation channel, which can be activated at physiological membrane potentials by stimuli including noxious heat (>42 degrees), capsaicin, hydrogen ions and anandamide. Activation of TRPV1 results in release of neurotransmitters from peripheral and central nerve terminals, resulting in pain and inflammation. Endogenous inflammatory mediators also promote activation of TRPV1. Studies in TRPV1 null mice reveal that responses to noxious heat stimuli are normal but the development of thermal hyperalgesia is abolished. Several TRPV1 antagonists have recently been developed and reported to alleviate or reverse mechanical and thermal hyperalgesia associated with inflammatory pain. This review will examine the development of patented TRPV1 antagonists as a potential clinical treatment for the alleviation of pain associated with hyperalgesia and inflammation.
Ubiquitin-like Protein FAT10 Promotes the Invasion and Metastasis of Hepatocellular Carcinoma by Modifying β-Catenin Degradation (2014)

The ubiquitin-like protein FAT10 and the homeobox protein HOXB9 each promote metastatic progression in hepatocellular carcinoma (HCC). In this study, we investigated the clinicopathologic significance of FAT10 and HOXB9 in HCC and investigated a mechanistic role for FAT10 in HOXB9-mediated invasiveness and metastasis. Relative to adjacent normal tissues, FAT10 and HOXB9 were markedly overexpressed in HCC, where a positive correlation in their expression and associated malignant characteristics were found. RNAi-mediated silencing of FAT10 decreased HOXB9 expression and inhibited HCC invasion and metastasis in vitro and in vivo. The effects of FAT10 silencing were reversed by HOXB9 overexpression, whereas RNAi-mediated silencing of HOXB9 decreased HCC invasion and metastasis driven by FAT10 overexpression. Mechanistically, FAT10 regulated HOXB9 expression by modulating the β-catenin/TCF4 pathway, directly binding to β-catenin and preventing its ubiquitination and degradation. Together, our results identified a novel HCC regulatory circuit involving FAT10, β-catenin/TCF4, and HOXB9, the dysfunction of which drives invasive and metastatic character in HCC. Cancer Res; 74(18); 5287-300. ©2014 AACR.
4:2:1 conduction of an AF initiating trigger (2015)

A 44 year old male with idiopathic dilated cardiomyopathy was undergoing persistent atrial fibrillation (AF) ablation. Following antral ablation, AF terminated into a regular narrow complex rhythm. Earliest activation was mapped to a focus in the superior vena cava (SVC) which was conducted in a 2:1 ratio to the atria which in turn was conducted with 2:1 ratio to the ventricles, resulting in an unusual 4:2:1 conduction of the SVC tachycardia. 1:1 conduction of the SVC tachycardia to the atrium preceded initiation of AF. During AF, SVC tachycardia continued unperturbed. Sinus rhythm was restored following catheter ablation of the focus.
MD-2-mediated Ionic Interactions between Lipid A and TLR4 Are Essential for Receptor Activation (2009)

Lipopolysaccharide (LPS) activates innate immune responses through TLR4.MD-2. LPS binds to the MD-2 hydrophobic pocket and bridges the dimerization of two TLR4.MD-2 complexes to activate intracellular signaling. However, exactly how lipid A, the endotoxic moiety of LPS, activates myeloid lineage cells remains unknown. Lipid IV(A), a tetra-acylated lipid A precursor, has been used widely as a model for lipid A activation. For unknown reasons, lipid IV(A) activates proinflammatory responses in rodent cells but inhibits the activity of LPS in human cells. Using stable TLR4-expressing cell lines and purified monomeric MD-2, as well as MD-2-deficient bone marrow-derived macrophages, we found that both mouse TLR4 and mouse MD-2 are required for lipid IV(A) activation. Computational studies suggested that unique ionic interactions exist between lipid IV(A) and TLR4 at the dimerization interface in the mouse complex only. The negatively charged 4'-phosphate on lipid IV(A) interacts with two positively charged residues on the opposing mouse, but not human, TLR4 (Lys(367) and Arg(434)) at the dimerization interface. When replaced with their negatively charged human counterparts Glu(369) and Gln(436), mouse TLR4 was no longer responsive to lipid IV(A). In contrast, human TLR4 gained lipid IV(A) responsiveness when ionic interactions were enabled by charge reversal at the dimerization interface, defining the basis of lipid IV(A) species specificity. Thus, using lipid IV(A) as a selective lipid A agonist, we successfully decoupled and coupled two sequential events required for intracellular signaling: receptor engagement and dimerization, underscoring the functional role of ionic interactions in receptor activation.
Use of a selectable marker regulated by alpha interferon to obtain mutations in the signaling pathway. (1989)

We have selected mutations in genes encoding components of the signaling pathway for alpha interferon (IFN-alpha) by using a specially constructed cell line. The upstream region of the IFN-regulated human gene 6-16 was fused to the Escherichia coli guanine phosphoribosyltransferase (gpt) gene and transfected into hypoxanthine-guanine phosphoribosyltransferase-negative human cells. These cells express gpt only in the presence of IFN-alpha. They grow in medium containing hypoxanthine, aminopterin, and thymidine plus IFN and are killed by 6-thioguanine plus IFN. Two different types of mutants were obtained after treating the cells with mutagens. A recessive mutant, selected in 6-thioguanine plus IFN, was completely resistant to IFN-alpha but responded normally to IFN-gamma and, unexpectedly, partially to IFN-beta. A constitutive mutant, selected in hypoxanthine-aminopterin-thymidine alone, was abnormal in expressing endogenous genes in the absence of IFN. Both types revert infrequently, allowing selection for complementation of the defects by transfection.
Function of Histone Deacetylase 6 as a Cofactor of Nuclear Receptor Coregulator LCoR (2009)

Ligand-dependent corepressor LCoR was identified as a protein that interacts with the estrogen receptor alpha (ERalpha) ligand binding domain in a hormone-dependent manner. LCoR also interacts directly with histone deacetylase 3 (HDAC3) and HDAC6. Notably, HDAC6 has emerged as a marker of breast cancer prognosis. However, although HDAC3 is nuclear, HDAC6 is cytoplasmic in many cells. We found that HDAC6 is partially nuclear in estrogen-responsive MCF7 cells, colocalizes with LCoR, represses transactivation of estrogen-inducible reporter genes, and augments corepression by LCoR. In contrast, no repression was observed upon HDAC6 expression in COS7 cells, where it is exclusively cytoplasmic. LCoR binds to HDAC6 in vitro via a central domain, and repression by LCoR mutants lacking this domain was attenuated. Kinetic chromatin immunoprecipitation assays revealed hormone-dependent recruitment of LCoR to promoters of ERalpha-induced target genes in synchrony with ERalpha. HDAC6 was also recruited to these promoters, and repeat chromatin immunoprecipitation experiments confirmed the corecruitment of LCoR with ERalpha and with HDAC6. Remarkably, however, although we find evidence for corecruitment of LCoR and ERalpha on genes repressed by the receptor, LCoR and HDAC6 failed to coimmunoprecipitate, suggesting that they are part of distinct complexes on these genes. Although small interfering RNA-mediated knockdown of LCoR or HDAC6 augmented expression of an estrogen-sensitive reporter gene in MCF7 cells, unexpectedly their ablation led to reduced expression of some endogenous estrogen target genes. Taken together, these data establish that HDAC6 can function as a cofactor of LCoR but suggest that they may act in enhance expressing some target genes.
The capacity of low-density parity-check codes under message-passing decoding (2001)

We present a general method for determining the capacity of low-density parity-check (LDPC) codes under message-passing decoding when used over any binary-input memoryless channel with discrete or continuous output alphabets. Transmitting at rates below this capacity, a randomly chosen element of the given ensemble will achieve an arbitrarily small target probability of error with a probability that approaches one exponentially fast in the length of the code. (By concatenating with an appropriate outer code one can achieve a probability of error that approaches zero exponentially fast in the length of the code with arbitrarily small loss in rate.) Conversely, transmitting at rates above this capacity the probability of error is bounded away from zero by a strictly positive constant which is independent of the length of the code and of the number of iterations performed. Our results are based on the observation that the concentration of the performance of the decoder around its average performance, as observed by Luby et al. in the case of a binary-symmetric channel and a binary message-passing algorithm, is a general phenomenon. For the particularly important case of belief-propagation decoders, we provide an effective algorithm to determine the corresponding capacity to any desired degree of accuracy. The ideas presented in this paper are broadly applicable and extensions of the general method to low-density parity-check codes over larger alphabets, turbo codes, and other concatenated coding schemes are outlined.
[In vitro study of a new pancreatic enzyme with high lipase content in enteric coated microtablets]. (1993)

In vitro behaviour of the enteric-coating of a new pancreatic enzyme containing preparation in enteric-coated microtablets was evaluated, by incubating at 37 degrees C, under gentle agitation, the preparation under study in buffered gastric (pH 2, 3, 4, 5, 6) and in buffered duodenal juice (pH 3, 4, 5, 6, 7, 8) for 30, 60, 90, 120 minutes. Lipase and chymotripsin activities were measured at each time and pH in the solution and in the undissolved microtablets. The drug under study showed a good enteric-coating, preserving about 100% of the enzyme content, when incubated in buffered gastric juice, up to pH 6, and releasing in the solution, during incubation in buffered duodenal juice, 75% of its enzyme content at pH 7 and 8. Therefore, the pancreatic enzymes contained in this new enteric-coated microtablet preparation are well protected against inactivation from acid and are bioavailable for digestion of alimentary substrates at optimal or near optimal pH in duodenal juice.
Role of the ubiquitin ligase E6AP/UBE3A in controlling levels of the synaptic protein Arc (2013)

Inactivation of the ubiquitin ligase E6 associated protein (E6AP) encoded by the UBE3A gene has been associated with development of the Angelman syndrome. Recently, it was reported that in mice, loss of E6AP expression results in increased levels of the synaptic protein Arc and a concomitant impaired synaptic function, providing an explanation for some phenotypic features of Angelman syndrome patients. Accordingly, E6AP has been shown to negatively regulate activity-regulated cytoskeleton-associated protein (Arc) and it has been suggested that E6AP targets Arc for ubiquitination and degradation. In our study, we provide evidence that Arc is not a direct substrate for E6AP and binds only weakly to E6AP, if at all. Furthermore, we show that down-regulation of E6AP expression stimulates estradiol-induced transcription of the Arc gene. Thus, we propose that Arc protein levels are controlled by E6AP at the transcriptional rather than at the posttranslational level.
Register File Architecture Optimization in a Coarse-Grained Reconfigurable Architecture (2005)

This paper investigates the impact of the local and global register file architecture on a reconfigurable system based on the ADRES architecture. The register files consume a significant amount of area on the reconfigurable device, and their architecture has a strong impact on the performance. We found that the global registers should be tightly connected to as many functional units as possible, while the connection of the local register files to their neighbours is less critical. We found that the global register file should contain between 12 and 16 registers, while each local register file should only contain one or two registers. We used these results to propose a new architecture that has between 60% and 95% higher performance per unit area compared to the original architecture over the set of benchmarks.
Influence of Cholesterol on the Association of Plasma Proteins with Liposomes (1996)

The in vivo association of blood proteins with large unilamellar liposomes composed of saturated phosphatidylcholines was analyzed to determine the effect of membrane fluidity and hydrocarbon chain length on liposome-plasma protein interactions and liposome clearance. Liposomes composed of dimyristoylphosphatidylcholine (DMPC), dipalmitoylphosphatidylcholine (DPPC), distearoylphosphatidylcholine (DSPC), and diarachidoylphosphatidylcholine (DAPC) were administered via the lateral tail vein of CD-1 mice and were subsequently isolated from the blood at 2 min postinjection. The protein binding ability (PB, grams of protein bound per mole total lipid) of the liposomes was quantified and related to their circulation half-lives. Liposomes composed of long-chain saturated phospholipids that exist in the gel (frozen) state at 39 degrees C (DPPC,DSPC and DAPC) bound large quantities of blood proteins, in excess of 48 g of protein per mole total lipid, and were found to be rapidly cleared from the circulation. The incorporation of cholesterol into DSPC liposomes resulted in significantly decreased PB values and enhanced circulation lifetimes for this lipid system. This cholesterol effect plateaued at 30 mol % cholesterol, corresponding to the loss of the gel-liquid crystalline phase transition, and resulted in PB values of 23-28 grams of protein per mole of total lipid. The types of blood proteins binding to DSPC liposomes were not significantly altered by the inclusion of cholesterol. This is the first demonstration of rapid clearance of neutral large unilamellar liposomes having high levels of bound protein.
Sensitivity to melphalan as a function of transport activity and proliferative rate in BALB/c 3T3 fibroblasts. (1987)

Melphalan transport by exponentially dividing BALB/c 3T3 mouse fibroblasts was approximately 3-fold greater at the steady-state than that observed with resting cells at drug concentrations ranging from 1 to 100 microM. Both the rate of incorporation of [3H]thymidine and the percentage of S-phase cells estimated by a fluorescent cell sorter provided evidence of higher DNA synthetic activity in logarithmic phase cells. Transport of melphalan by BALB/c 3T3 fibroblasts was mediated by the two amino acid transport systems, the DL-beta-2-aminobicyclo(2,2,1)heptane-2-carboxylic acid-sensitive sodium-independent system preferring leucine as substrate and the sodium-dependent system preferring alanine, serine, and cysteine as substrates. At low drug concentrations (about 1 microM) the sodium-dependent mechanism predominated, but at high concentrations of melphalan (100 microM) a shift occurred from the sodium-dependent to the sodium-independent system. Both transport systems were markedly affected by the proliferative state of the cells and became progressively less active the longer cells remained in the stationary phase. Stationary-phase cells were also less sensitive to the cytotoxic action of melphalan than exponentially dividing cells. Serum deprivation experiments showed that unidirectional melphalan influx decreased about 40% when fibroblasts previously in exponential growth were shifted from normal medium to serum-depleted medium 24 h prior to drug transport studies. Thus, serum deprivation and maintenance of cells in stationary phase growth had parallel effects on drug influx. These experiments emphasize the importance of the proliferative state of the cell as a determinant of melphalan transport and cytocidal activity.
Self-Cleavable Stimulus Responsive Tags for Protein Purification without Chromatography (2005)

A simple method to purify recombinant proteins is described by fusing a target protein with an intein and an elastin-like polypeptide that only requires NaCl, dithiothreitol, and a syringe filter to isolate the target protein from Escherichia coli lysate. This tripartite fusion system enables rapid isolation of the target protein without the need for affinity chromatography for purification or proteases for cleavage of the target protein from the fusion. The elastin-like polypeptide tag imparts reversible phase transition behavior to the tripartite fusion so that the fusion protein can be selectively aggregated in cell lysate by the addition of NaCl. The aggregates are isolated by microfiltration and resolubilized by reversal of the phase transition in low ionic strength buffer. After resolubilizing the fusion protein, the intein is activated to cleave the target protein from the elastin-intein tag, and the target protein is then isolated from the elastin-intein fusion by an additional phase transition cycle.