gebhart/patrepeval huggingface dataset:
Genesis field, Gulf of Mexico: Recognizing reservoir compartments on geologic and production time scales in deep-water reservoirs (2007)

In this study of the Genesis field, a deep-water Gulf of Mexico oil field, we used log, seismic, and preproduction pressure data to identify static reservoir compartments. Static compartments are defined by boundaries that, over geologic time, are barriers to fluid flow. Within a static compartment, the contact between two fluids will settle at a single elevation. We then evaluated production data, including pressure data from permanent downhole gauges, as a check on our static model and to identify dynamic compartments. Dynamic compartments are defined by boundaries that are not effective barriers to fluid flow over geologic time, but impede flow to the extent that they have a significant impact on contact movement or pressure depletion during production. Having defined static and dynamic compartments, we explored the stratigraphic and structural controls on these compartments in three deep-water reservoirs of Genesis field. The oldest of these, Neb 3, is interpreted as the deposits of an erosionally confined channel complex. Neb 3 has a common oil-water contact throughout the field. During production, Neb 3 development wells showed a common pressure decline trend and had moderate aquifer support. The Neb 2 reservoir is interpreted as the deposits of a muddier, more poorly amalgamated channel complex. At least two different original oil-water contacts were observed in this reservoir before the start of production. Production data also indicated greater compartmentalization in Neb 2 than that observed in Neb 3. Our preproduction analysis of the Neb 1 reservoir identified at least two different oil-water contacts. With production, multiple barriers and baffles to flow became apparent. Aquifer support ranged from moderate to none. We interpret Neb 1 as the deposits of a channel-levee complex. The connection between channels and levees in Neb 1 appears to be poor. Overall, the stratigraphic architecture of these reservoirs was the underlying control on the degree of compartmentalization over both geologic and production time scales, with structure (faulting) exerting a lesser control and primarily acting to enhance vertical connectivity between reservoirs via juxtaposition.
Rhinoviruses Induce Interleukin-8 mRNA and Protein Production in Human Monocytes (1997)

Rhinoviruses are important upper respiratory pathogens that are strongly associated with asthma exacerbations. However, the inflammatory response to rhinovirus infection is poorly understood. Interleukin (IL)-8 has been implicated in the pathogenesis of respiratory viral infections and asthma. Rhinovirus-induced IL-8 release and mRNA induction were examined in peripheral blood mononuclear cells (PBMC). Rhinoviruses induced IL-8 release for up to 7 days after inoculation onto PBMC. This was associated with an increase in IL-8 mRNA expression that peaked 48 h after exposure to the virus. IL-8 protein production was reduced by UV inactivation of the virus and abolished by preventing virus-receptor binding. Although rhinovirus replication was not demonstrated in PBMC, low-grade productive infection was shown in the human monocyte cell line THP-1. Rhinovirus induction of IL-8 in monocytes or airway macrophages may be important in the pathogenesis of rhinovirus-induced asthma exacerbation.
2,3,7,8-Tetrachlorodibenzo-p-dioxin poly(ADP-ribose) polymerase (TiPARP, ARTD14) is a mono-ADP-ribosyltransferase and repressor of aryl hydrocarbon receptor transactivation (2012)

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD)-inducible poly(ADP-ribose) polymerase (TiPARP/ARTD14) is a member of the PARP family and is regulated by the aryl hydrocarbon receptor (AHR); however, little is known about TiPARP function. In this study, we examined the catalytic function of TiPARP and determined its role in AHR transactivation. We observed that TiPARP exhibited auto-mono-ADP-ribosyltransferase activity and ribosylated core histones. RNAi-mediated knockdown of TiPARP in T-47D breast cancer and HuH-7 hepatoma cells increased TCDD-dependent cytochrome P450 1A1 (CYP1A1) and CYP1B1 messenger RNA (mRNA) expression levels and recruitment of AHR to both genes. Overexpression of TiPARP reduced AHR-dependent increases in CYP1A1-reporter gene activity, which was restored by overexpression of AHR, but not aryl hydrocarbon receptor nuclear translocator. Deletion and mutagenesis studies showed that TiPARP-mediated inhibition of AHR required the zinc-finger and catalytic domains. TiPARP and AHR co-localized in the nucleus, directly interacted and both were recruited to CYP1A1 in response to TCDD. Overexpression of Tiparp enhanced, whereas RNAi-mediated knockdown of TiPARP reduced TCDD-dependent AHR proteolytic degradation. TCDD-dependent induction of AHR target genes was enhanced in Tiparp(-/-) mouse embryonic fibroblasts compared with wildtype controls. Our findings show that TiPARP is a mono-ADP-ribosyltransferase and a transcriptional repressor of AHR, revealing a novel negative feedback loop in AHR signalling.
SAT-169 Selective Nonpeptide Somatostatin Subtype 5 (sst5) Agonists Suppress Glucose- and Sulfonylurea-Induced Insulin Secretion in Rats (2019)

Congenital hyperinsulinism (CHI) results from mutations within the insulin secretion pathway and is characterized by excessive and/or inappropriate insulin secretion by pancreatic islet β-cells. CHI is the most common cause of persistent hypoglycemia in newborns and infants and is estimated to affect 1/30,000 to 1/50,000 live births. Prompt recognition and treatment are vital to prevent coma, long-term neurological complications, and even death. If medical control of CHI is unsuccessful, near-total pancreatectomy may be required. The neuropeptide somatostatin is an important modulator of pancreatic hormonal signaling and activity at different somatostatin receptor (sst) subtypes dictates the suppression of insulin and/or glucagon. Glucagon secretion from α-cells is inhibited through sst2 receptors and insulin secretion from β-cells is inhibited through activation of sst2, sst3, and sst5. The injectable peptide drugs octreotide and lanreotide are potent agonists at sst2 and are often deployed as the last medical intervention to prevent or delay pancreatectomy. These peptides’ sst2 activity leads to inhibition of glucagon secretion, potentially reducing their effectiveness and compromising a key defense mechanism against hypoglycemia. We hypothesize that agonists targeting sst5 but lacking sst2 activity will possess an optimal efficacy/safety profile for patients with hyperinsulinemic hypoglycemia. Using iterative medicinal chemistry, Crinetics has discovered several classes of highly potent, orally bioavailable, small molecule sst-subtype selective agonists with drug-like pharmaceutical properties. Our discovery efforts aimed at finding a compound to treat CHI have yielded potent and selective nonpeptide sst5 agonists with sub-nanomolar EC50s in cell-based assays of receptor activation. These compounds also typically possess similar potency for the rat sst5 receptor. To probe their physiological consequences and to gain mechanistic insights, we compared the acute and chronic effects of these agonists to the peptide pasireotide, a pan-sst agonist that is most potent at sst5, on glycemic control in several rat models, which generally demonstrate a high degree of translation to humans. These preclinical studies evaluated the effects of the sst5 agonists during oGTT, ipGTT, sulfonylurea-induced hypoglycemia, and on blood glucose levels in both the fed and fasted states. In each model, selective nonpeptide sst5 agonists suppressed insulin secretion and raised blood glucose levels while having minimal effects on glucagon secretion, as predicted by their in vitro pharmacology. These results support our efforts to develop potent nonpeptide selective sst5 agonists with pharmaceutical and safety profiles suitable for evaluation in human clinical trials.
AUUUA is not sufficient to promote poly(A) shortening and degradation of an mRNA: the functional sequence within AU-rich elements may be UUAUUUA(U/A)(U/A). (1994)

AU-rich elements (AREs) in the 3' untranslated regions of several cytokine and oncogene mRNAs have been shown to function as signals for rapid mRNA degradation, and it is assumed that the many other cytokine and oncogene mRNAs that contain AU-rich sequences in the 3' untranslated region are similarly targeted for rapid turnover. We have used a chimeric gene composed mostly of growth hormone sequences with expression driven by the c-fos promoter to investigate the minimal sequence required to act as a functional destabilizing element and to monitor the effect of these sequences on early steps in the degradation pathway. We find that neither AUUUA, UAUUUA, nor AUUUAU can function as a destabilizing element. However, the sequence UAUUUAU, when present in three copies, is sufficient to destabilize a chimeric mRNA. We propose that this sequence functions by virtue of being a sufficient portion of the larger sequence, UUAUUUA(U/A)(U/A), that we propose forms the optimal binding site for a destabilizing factor. The destabilizing effect depends on the number of copies of this proposed binding site and their degree of mismatch in the first two and last two positions, with mismatches in the AUUUA sequence not being tolerated. We found a strict correlation between the effect of an ARE on degradation rate and the effect on the rate of poly(A) shortening, consistent with deadenylation being the first and rate-limiting step in degradation, and the step stimulated by destabilizing AREs. Deadenylation was observed to occur in at least two phases, with an oligo(A) intermediate transiently accumulating, consistent with the suggestion that the degradation processes may be similar in yeast and mammalian cells. AREs that are especially U rich and contain no UUAUUUA(U/A)(U/A) motifs failed to influence the degradation rate or the deadenylation rate, either when downstream of suboptimal destabilizing AREs or when alone.
Monoclonal antibody defining a stage-specific mouse embryonic antigen (SSEA-1). (1978)

A monoclonal antibody derived by fusion of mouse myeloma cells with spleen cells from a mouse immunized with F9 teratocarcinoma cells is described. This antibody, which reacts with embryonal carcinoma cells of mouse and human origin and with some preimplantation stage mouse embryos, defines an embryonic stage-specific antigen. This stage-specific antigen (SSEA-1) is first detected on blastomeres of 8-cell stage embryos. Trophectodermal cells are transitorily positive; however, each cell in the inner cell mass eventually expresses this antigen.
Comparison of flow cytometry and laser scanning cytometry for the analysis of CD34+ hematopoietic stem cells (2004)

LSC-based analysis allows for the automated evaluation of adherent HSCs. Although resolution of weakly expressed antigens can be achieved more precisely with FCM, the method provides a valuable tool to study interactions of HSCs with bioartificial substrates.
Investigation of Specific Binding Proteins to Photoaffinity Linkers for Efficient Deconvolution of Target Protein (2015)

Photoaffinity-based target identification has received recent attention as an efficient research tool for chemical biology and drug discovery. The major obstacle of photoaffinity-based target identification is the nonspecific interaction between target identification probes and nontarget proteins. Consequently, the rational design of photoaffinity linkers has been spotlighted for successful target identification. These nonspecific interactions have been considered as random events, and therefore no systematic investigation has been conducted regarding nonspecific interactions between proteins and photoaffinity linkers. Herein, we report the protein-labeling analysis of photoaffinity linkers containing three photoactivatable moieties: benzophenone, diazirine, and arylazide. Each photoaffinity linker binds to a different set of proteins in a structure-dependent manner, in contrast to the previous conception. The list of proteins labeled by each photoaffinity linker was successfully used to eliminate the nonspecific binding proteins from target candidates, thereby increasing the success rate of target identification.
Stabilization of Ceramic Strain Gages to Temperatures beyond 1500°C (2003)

The stability of thin film strain gages based on indium-tin-oxide (ITO), at temperature approaching 1500°C, was discussed. High temperature static strain tests indicated that the piezoresistive response and electrical stability depend on the thickness of ITO films comprising the active strain element of these sensors. Sputtered ITO films, doped with aluminum were stable in air to temperatures in excess of 1530 °C. It was found that aluminum doping of the ITO film appears to create a barrier around the ITO structures, which helps to resist oxidation and further stabilizes the ITO thin film at elevated temperatures.
P56lck: a transducing protein that binds to SH2 containing proteins and to phosphotyrosine containing proteins. (1994)

In T lymphocytes, several proteins are rapidly phosphorylated on tyrosine after stimulation. In this study we examine the ability of tyrosine phosphorylated proteins from Jurkat T cells stimulated by CD2 or T cell receptor (TcR)-CD3 to interact with the src homology 2 (SH2) domains from p56lck (Lck). Our data show that the patterns are different depending on the stimulation. The specificity of the interactions was assessed by blocking experiments with high affinity phosphotyrosine [Y(P)] peptides. Phosphorylation experiments suggest that one or several kinases are able to interact with the SH2 from Lck. On the other hand, full length Lck overexpressed in Sf9 cells, which is tyrosine-phosphorylated at least on two sites, can interact in vitro with the SH2 from Lck, phospholipase C (PLC)-gamma 1, p85 (the regulatory subunit of phosphatidyl-inositol-3 kinase (PI3K)) and Nck and with the full length Grb2. These data give additional support to the idea that Lck is an important signal transducing molecule in lymphocytes.
Ex Vivo Normothermic Perfusion Induces Donor-Derived Leukocyte Mobilization and Removal Prior to Renal Transplantation (2016)

We demonstrate that <i>ex vivo</i> normothermic perfusion initiates an inflammatory cytokine storm and release of mitochondrial and genomic DNA. This is likely to be responsible for immune cell activation and mobilization into the circuit prior to transplantation. Interestingly this did not have an impact on renal function. These data therefore suggest that normothermic perfusion can be used to immunodeplete and to saturate the pro-inflammatory capacity of donor kidneys prior to transplantation.
A Fifth Pathway of Carbon Fixation (2007)

Biofouling and biocorrosion by microbiota from a marine oil pipeline: A metagenomic and proteomic approach,
Detection of Trace Heavy Metal Ions Using Carbon Nanotube‐ Modified Electrodes (2009)

Abstract A sensitive voltammetric method for detection of trace heavy metal ions using chemically modified carbon nanotubes (CNTs) electrode surfaces is described. The CNTs were covalently modified with cysteine prior to casting on electrode surfaces. Cysteine is an amino acid with high affinities towards some heavy metals. In this assay, heavy metals ions accumulated on the cysteine‐modified CNT electrode surfaces prior to being subjected to differential pulse anodic stripping voltammetry analysis. The resulting peak currents were linearly related to the concentrations of the metal ions. The method was optimized with respect to accumulation time, reduction time and reduction potential. The detection limits were found to be 1 ppb and 15 ppb for Pb 2+ and Cu 2+ respectively. The technique was used for the detection of Pb 2+ and Cu 2+ in spiked lake water. The average recoveries of Pb 2+ and Cu 2+ were 96.2% and 94.5% with relative standard deviations of 8.43% and 7.53% respectively. The potential for simultaneous detection of heavy metal ions by the modified CNTs was also demonstrated.
Stemness Evaluation of Mesenchymal Stem Cells from Placentas According to Developmental Stage: Comparison to Those from Adult Bone Marrow (2010)

This study was done to evaluate the stemness of human mesenchymal stem cells (hMSCs) derived from placenta according to the development stage and to compare the results to those from adult bone marrow (BM). Based on the source of hMSCs, three groups were defined: group I included term placentas, group II included first-trimester placentas, and group III included adult BM samples. The stemness was evaluated by the proliferation capacity, immunophenotypic expression, mesoderm differentiation, expression of pluripotency markers including telomerase activity. The cumulative population doubling, indicating the proliferation capacity, was significantly higher in group II (P<0.001, 31.7±5.8 vs. 15.7±6.2 with group I, 9.2±4.9 with group III). The pattern of immunophenotypic expression and mesoderm differentiation into adipocytes and osteocytes were similar in all three groups. The expression of pluripotency markers including ALP, SSEA-4, TRA-1-60, TRA-1-81, Oct-4, and telomerase were strongly positive in group II, but very faint positive in the other groups. In conclusions, hMSCs from placentas have different characteristics according to their developmental stage and express mesenchymal stemness potentials similar to those from adult human BMs.
New Oral Dosage Form for Elderly Patients. II. Release Behavior of Benfotiamine from Silk Fibroin Gel. (1995)

Silk fibroin gel (SFG) containing benfotiamine (BTMP) was prepared. The release behavior of BTMP from SFG was studied as a function of silk fibroin (SF) content and glycerol content, and the influence of the existence of beta-cyclodextrin (beta-CD) on the physicochemical properties of SFG were investigated. The release rate of BTMP from SFG was retarded by an increase in SF concentration. The addition of beta-CD affected both the release properties and rheological properties of the SFG. It was found from the results of the "paddle-bead method" that the release profiles of BTMP from SFG were inversely proportional to the SFG firmness.
COX-2 selective inhibitors cardiac toxicity: getting to the heart of the matter. (2004)

On September 30, 2004, Merck and Co. voluntary withdrew rofecoxib (Vioxx) from the market due to increased risk of cardiovascular events associated with the drug. This raised some issues. It is unclear whether the cardiac toxicities associated with rofecoxib isare due to its high COX-2 selectivity. Rofecoxib is the most specific COX-2 inhibitor among the first generation of the class, i.e., negligible COX-1 inhibitory effect. In addition to the gastrointestinal side effects, COX-1 inhibition is known to offer cardioprotection. This is one of the main present indications of aspirin-like drugs. It is plausible that the COX-2 inhibition is associated with altered homeostasis that is compensated with the cardioprotection effect of COX-1 inhibition that patients receive either through the less COX-2 selectivity of other NSAIDs or through co-administration of low dose aspirin. In addition, the cardiac toxicity of rofecoxib could be due to its unique chemical structure, its pharmacokinetics and tissue distribution, and/or the presence of toxic metabolites. Nevertheless, one cannot ignore the public need for NSAIDs with less gastrointestinal side effects than the traditional drugs. However, based on some available indirect evidence, and unless more clear-cut data become available, the use of highly COX-2 selective NSAIDs without the use of a suitable COX-1 inhibitor, (e.g., low dose aspirin) may be best avoided. This may be particularly relevant to the chronic use of these drugs.
Induction of Epstein-Barr virus-associated DNA polymerase by 12-O-tetradecanoylphorbol-13-acetate. Purification and characterization. (1980)

The diterpene ester promoter of mouse skin tumors, 12-O-tetradecanoylphorbol-13-acetate (TPA), efficiently induces Epstein-Barr virus (EBV)-associated DNA polymerase (DNA nucleotidyltransferase) activity in the EBV-producing lymphoblastoid cell line, P3HR-1. With the use of intervent dilution chromatography followed by sequential DEAE-cellulose and phosphocellulose column chromatography, the virus-associated enzyme has been isolated and purified 300-fold. The partially purified EBV DNA polymerase activity could be distinguished from cellular polymerases by its activation with salt and its degree of sensitivity to N-ethylmaleimide and phosphonoacetic acid. The enzyme showed maximum activity for copying activated calf thymus DNA in the presence of 100 mM ammonium sulfate. In the absence of salt, the enzyme utilized with high efficiency deoxyoligomer-homopolymer templates, but failed to copy poly(rA) . oligo(dT)10 and oligo(dT)10, showing that the enzyme had properties distinct from DNA polymerase gamma, reverse transcriptase, and terminal deoxynucleotidyltransferase. The partially purified enzyme is strongly inhibited by acyclovir triphosphate and thus has properties similar to herpes simplex virus DNA polymerase.
Polyphenols and Human Health: Prevention of Disease and Mechanisms of Action (2010)

Polyphenols are found ubiquitously in plants and their regular consumption has been associated with a reduced risk of a number of chronic diseases, including cancer, cardiovascular disease (CVD) and neurodegenerative disorders. Rather than exerting direct antioxidant effects, the mechanisms by which polyphenols express these beneficial properties appear to involve their interaction with cellular signaling pathways and related machinery that mediate cell function under both normal and pathological conditions. We illustrate that their interactions with two such pathways, the MAP kinase (ERK, JNK, p38) and PI3 kinase/Akt signaling cascades, allow them to impact upon normal and abnormal cell function, thus influencing the cellular processes involved in the initiation and progression of cancer, CVD and neurodegeneration. For example, their ability to activate ERK in neurons leads to a promotion of neuronal survival and cognitive enhancements, both of which influence the progression of Alzheimer's disease, whilst ERK activation by polyphenols in vascular endothelial cells influences nitric oxide production, blood pressure and ultimately CVD risk. The main focus of this review is to provide an overview of the role that polyphenols play in the prevention of cancer, cardiovascular disease and neurodegeneration. We present epidemiological data, human intervention study findings, as well as animal and in vitro studies in support of these actions and in each case we consider how their actions at the cellular level may underpin their physiological effects.