gebhart/patrepeval huggingface dataset:
The Death Ligand TRAIL in Diabetic Nephropathy (2008)

Apoptotic cell death contributes to diabetic nephropathy (DN), but its role is not well understood. The tubulointerstitium from DN biopsy specimens was microdissected, and expression profiles of genes related to apoptosis were analyzed. A total of 112 (25%) of 455 cell death-related genes were found to be significantly differentially regulated. Among those that showed the greatest changes in regulation were two death receptors, OPG (the gene encoding osteoprotegerin) and Fas, and the death ligand TRAIL. Glomerular and proximal tubular TRAIL expression, assessed by immunohistochemistry, was higher in DN kidneys than controls and was associated with clinical and histologic severity of disease. In vitro, proinflammatory cytokines but not glucose alone regulated TRAIL expression in the human proximal tubular cell line HK-2. TRAIL induced tubular cell apoptosis in a dosage-dependant manner, an effect that was more marked in the presence of high levels of glucose and proinflammatory cytokines. TRAIL also activated NF-kappaB, and inhibition of NF-kappaB sensitized cells to TRAIL-induced apoptosis. It is proposed that TRAIL-induced cell death could play an important role in the progression of human DN.
Transient Focal Ischemia Increases Endothelial Nitric Oxide Synthase in Cerebral Blood Vessels (2002)

eNOS protein is upregulated in pre- and postcapillary microvessels and upregulation appears slower after transient compared with permanent ischemia. Cyclooxygenase and NOS products do not play a major role in postischemic eNOS induction.
Correction of a human beta S-globin gene by gene targeting. (1991)

As a step toward using gene targeting for gene therapy, we have corrected a human beta S-globin gene to the normal beta A allele by homologous recombination in the mouse-human hybrid cell line BSM. BSM is derived from a mouse erythroleukemia cell line and carries a single human chromosome 11 with the beta S-globin allele. A beta A-globin targeting construct containing a unique oligomer and a neomycin-resistance gene was electroporated into the BSM cells, which were then placed under G418 selection. Then 126 resulting pools containing a total of approximately 29,000 G418-resistant clones were screened by PCR for the presence of a targeted recombinant: 3 positive pools were identified. A targeted clone was isolated by replating one of the positive pools into smaller pools and rescreening by PCR, followed by dilution cloning. Southern blot analysis demonstrated that the isolated clone had been targeted as planned. The correction of the beta S allele to beta A was confirmed both by allele-specific PCR and by allele-specific antibodies. Expression studies comparing the uninduced and induced RNA levels in unmodified BSM cells and in the targeted clone showed no significant alteration in the ability of the targeted clone to undergo induction, despite the potentially disrupting presence of a transcriptionally active neomycin gene 5' to the human beta A-globin gene. Thus gene targeting can correct a beta S allele to beta A, and the use of a selectable helper gene need not significantly interfere with the induction of the corrected gene.
Removal of Dibenzofuran, Dibenzo- p -Dioxin, and 2-Chlorodibenzo- p -Dioxin from Soils Inoculated with Sphingomonas sp. Strain RW1 (1999)

Removal of dibenzofuran, dibenzo-p-dioxin, and 2-chlorodibenzo-p-dioxin (2-CDD) (10 ppm each) from soil microcosms to final concentrations in the parts-per-billion range was affected by the addition of Sphingomonas sp. strain RW1. Rates and extents of removal were influenced by the density of RW1 organisms. For 2-CDD, the rate of removal was dependent on the content of soil organic matter (SOM), with half-life values ranging from 5.8 h (0% SOM) to 26.3 h (5.5% SOM).
Bradycardia During Dexmedetomidine and Therapeutic Hypothermia (2008)

Dexmedetomidine is a centrally acting alpha2-adrenergic agonist which is currently Food and Drug Administration-approved for the short-term (less than 24 hours) sedation of adults during mechanical ventilation. Given its beneficial physiologic effects and limited adverse effect profile, there is growing interest regarding its potential applications in the Pediatric intensive care unit patient including sedation during mechanical ventilation, procedural sedation, the treatment of withdrawal, and prevention of emergence agitation. Although generally safe and effective, occasional hemodynamic effects including bradycardia and hypotension have been reported. Clinical experience has demonstrated that bradycardia may be more common when dexmedetomidine is administered with other medications that have negative chronotropic effects. We report 2 pediatric patients with traumatic brain injury who had good long-term neurologic outcomes, but developed clinically significant bradycardia when therapeutic hypothermia was added to a sedation regimen that included dexmedetomidine and remifentanil. The role of dexmedetomidine as a neuroprotective agent is explored as well as a review presented of previous reports of bradycardia related to dexmedetomidine.
Co(salen)-Catalyzed tert-Butyl Hydroperoxide Oxidation of tert-Butylphenols Bearing an Unsaturated Side Chain (1996)

Co(salen)-catalyzed oxidation of 2,4- and 2,6-di-tert-butylphenols bearing an unsaturated side chain, with tert-butyl hydroperoxide (TBHP) in CH2Cl2 at rt, results predominantly in the formation of tert-butylperoxylated products. The position of tert-butylperoxylation depends on the nature of the unsaturated side chain: predominantly the ortho position for 4-alkynyl-2,6-di-tert-butylphenols, the side chain for 4-alkenyl-2,6-di-tert-butylphenols, and the para position for 4-cyano- or 4-(1-methoxyimino)alkyl-2,6-di-tert-butylphenols as well as 2-alkynyl-, 2-alkenyl-, and 2-cyano-4,6-di-tert-butylphenols. The ortho tert-butylperoxylated products arise mainly from initially formed para tert-butylperoxylated products, by migration of the tert-butylperoxy group.
The promoter of the Arabidopsis thaliana plastocyanin gene contains a far upstream enhancer‐like element involved in chloroplast‐dependent expression (1993)

Plastocyanin is part of the photosynthetic electron transport chain in the chloroplast and is encoded in the nucleus. Expression of the Arabidopsis thaliana plastocyanin gene is organ specific: high mRNA levels are observed in young green parts of the plant. Furthermore, expression is dependent on the presence of light and functional chloroplasts. When grown in the presence of norflurazon under white light conditions, resulting in the photo-oxidative destruction of the chloroplast, plastocyanin mRNA levels are strongly reduced. A -1579 to -9 promoter fragment confers light-regulated and chloroplast-dependent expression to the beta-glucuronidase reporter gene in transgenic tobacco plants. This suggests that regulation takes place at the level of transcription. A plastocyanin promoter deletion series ranging from -1579 to -121 which was also tested in tobacco, revealed the presence of a strong positive regulating element (PRE) in the -1579 to -705 region. Deletion of this part of the promoter resulted in a approximately 100-fold reduction of GUS expression as measured in mature leaves. Surprisingly, this enhancer-like element was capable of stimulating transcription from a position downstream of its reporter. Moreover, it could also activate a truncated CaMV 35S promoter. Deletion of this element coincides with the loss of chloroplast-dependency of reporter gene expression, as judged by norflurazon treatment of transgenic seedlings. So, the activity of the PRE itself might depend on the presence of functional chloroplasts.
Routability checking for three-dimensional architectures (2004)

We present a novel symbolic routability checking approach for three-dimensional interconnect layout. The model considered is a general architecture that can fit into different applications, such as ASIC, multichip modules, field-programmable gate arrays, and reconfigurable computing architectures. The method can incrementally incorporate additional constraints driven by timing, performance, and design. We used the latest satisfiability solver to validate the effectiveness of our approach. The experimental results demonstrate the encouraging performance on difficult routing benchmarks.
Management of Wound Complications From Cesarean Delivery (2005)

After completion of this article, the reader should be able to describe the effects of obesity on cesarean delivery wound healing, to improve methods of wound healing in the obese patient, and to explain why wet to dry dressing changes are not effective wound management.
Generation of specific cytotoxic T cells with a fragment of the Epstein-Barr virus-encoded p63/latent membrane protein. (1987)

Human B lymphocytes, transformed by the herpesvirus Epstein-Barr virus, are known to express a characteristic antigen(s) recognized by the cellular immune response. This structure has been termed lymphocyte-determined membrane antigen. Because of the significance of this structure in controlling Epstein-Barr virus infection in vivo, the molecular nature of lymphocyte-determined membrane antigen has been long sought. In this paper, we show that a sequence of 10 amino acids (residues 43-53) from the Epstein-Barr virus-encoded membrane protein p63/latent membrane protein can induce Epstein-Barr virus-specific cytotoxic T cells and, therefore, bears at least one of the lymphocyte-determined membrane antigenic determinants.
Gene Expression and Antiviral Activity of Alpha/Beta Interferons and Interleukin-29 in Virus-Infected Human Myeloid Dendritic Cells (2005)

Dendritic cells (DCs) respond to microbial infections by undergoing phenotypic maturation and by producing multiple cytokines. In the present study, we analyzed the ability of influenza A and Sendai viruses to induce DC maturation and activate tumor necrosis factor alpha (TNF-alpha), alpha/beta interferon (IFN-alpha/beta), and IFN-like interleukin-28A/B (IFN-lambda2/3) and IL-29 (IFN-lambda1) gene expression in human monocyte-derived myeloid DCs (mDC). The ability of influenza A virus to induce mDC maturation or enhance the expression of TNF-alpha, IFN-alpha/beta, interleukin-28 (IL-28), and IL-29 genes was limited, whereas Sendai virus efficiently induced mDC maturation and enhanced cytokine gene expression. Influenza A virus-induced expression of TNF-alpha, IFN-alpha, IFN-beta, IL-28, and IL-29 genes was, however, dramatically enhanced when cells were pretreated with IFN-alpha. IFN-alpha priming led to increased expression of Toll-like receptor 3 (TLR3), TLR7, TLR8, MyD88, TRIF, and IFN regulatory factor 7 (IRF7) genes and enhanced influenza-induced phosphorylation and DNA binding of IRF3. Influenza A virus also enhanced the binding of NF-kappaB to the respective NF-kappaB elements of the promoters of IFN-beta and IL-29 genes. In mDC IL-29 induced MxA protein expression and possessed antiviral activity against influenza A virus, although this activity was lower than that of IFN-alpha or IFN-beta. Our results show that in human mDCs viruses can readily induce the expression of IL-28 and IL-29 genes whose gene products are likely to contribute to the host antiviral response.
Developmental and Hormonal Regulation of Bovine Granulosa Cell Function in the Preovulatory Follicle* (1988)

Bovine granulosa cells were isolated from small antral, medium antral, and large Graffian follicles (i.e. small, medium, and large preovulatory follicles). Serum-free cultures of granulosa cells were established and found to be viable for 3-6 days of cell culture. Radiolabeled granulosa cell-secreted proteins were obtained and analyzed electrophoretically. No major changes were detected in the protein profiles of small, medium, and large follicle granulosa cells. FSH and insulin, however, had a dramatic effect on granulosa cell-secreted proteins and increased the apparent production of 200K, 65K, 25K, and 15K proteins. The effects of these hormones on the radiolabeled secreted proteins were similar for small, medium, and large follicle granulosa cells. Aromatase activity was high for the first day of serum-free granulosa cell culture and subsequently declined to low levels. Both FSH and insulin alone stimulated aromatase activity, while a combination of hormones resulted in an additive response similar to the stimulation observed with 10% calf serum. Although the level of aromatase activity increased slightly with the size of the follicle, the effects of hormones were independent of follicle size. Progesterone production was low on days 1 and 2 of serum-free granulosa cell culture and high on days 3 and 6 of cell culture. Interestingly, FSH and insulin suppressed progesterone production on day 1 of cell culture for small and medium follicle granulosa cells, but not for large follicle cells. In contrast, hormones stimulated progesterone production on days 3 and 6 of granulosa cell culture, and the level of progesterone production increased with the size of the follicle. The stimulatory effects of hormones on days 3 and 6 of the culture were similar for medium and large follicle granulosa cells, but were altered for small follicle cells. Results indicate that when aromatase activity is high and stimulated by hormones, progesterone levels are low and generally suppressed by the same regulatory agents. Conversely when progesterone levels are high and hormone responsive, aromatase activity is low. The inverse relationship between aromatase activity and progesterone production implies that bovine granulosa cells alter their differentiated state in culture from an estrogen-producing cell to a progesterone-producing cell. Combined observations indicate that the results obtained on day 1 of culture probably reflect the developmental and hormonal regulation of granulosa cell function in the preovulatory follicle, while data obtained at later times in culture reflect the ability of the cell to synthesize progesterone and develop a luteinization-like activity.(ABSTRACT TRUNCATED AT 400 WORDS)
A fuzzy processing for respiratory rate monitoring system by optical fiber sensor (2008)

This paper describes a fuzzy processing method for a respiratory rate monitoring system by an optical fiber sensor. This optical fiber sensor has a part of sensor sheet and a polarization detector. It noninvasively detects vital signal of human on the sheet by obtaining polarization variations. By using this sensor, we propose a fuzzy processing method of a respiratory rate for human in the bed. Our method was tested on five volunteers. We successfully detected a respiratory rate. In it, fuzzy logic plays a primary role in the detection. Our system determines fuzzy membership functions by using characteristic of respiration. Consequently, this system can noninvasively detect a respiratory rate by using a constraint-free device.
Chromosomal localization and characterization of c-abl in the t(6;9) of acute nonlymphocytic leukemia. (1985)

Acute nonlymphocytic leukemia associated with the chromosomal translocation t(6;9)(p23;q34) is an entity that is frequently associated with basophilia, which it shares with chronic myelogenous leukemia. The breakpoint on chromosome 9, q34, appears to be cytogenetically identical in both malignancies and is the site of the cellular oncogene c-abl. We investigated the role of c-abl in cells from two patients with the t(6;9) using in situ chromosomal hybridization, Southern hybridization, and in vitro phosphorylation. We showed that c-abl is not translocated from chromosome 9, resulting in a breakpoint that is on the 3' side of this gene. The t(6;9) translocation does not appear to result in the production of an aberrantly sized protein product or in the acquisition of in vitro tyrosine kinase activity. This is in direct contrast to the findings in chronic myelogenous leukemia, in which c-abl is translocated, leading to the production of a structurally altered c-abl protein with activated tyrosine kinase. Lastly, we demonstrated that the cells of one patient contain sequences from chromosome 9 inserted at the junction of a reciprocal translocation between chromosomes 4 and 10 on the 4q+ chromosome. This insertion, which is at least 100 kilobase pairs in length, represents a duplication and translocation of the protein coding region of c-abl.
Cytokines fused to antibodies and their combinations as therapeutic agents against different peritoneal HER2/ neu expressing tumors (2006)

We have previously generated antihuman HER2/neu-humanized IgG3 fused to interleukin-2 (IL-2), IL-12, or granulocyte macrophage colony-stimulating factor (GM-CSF) [monofunctional fusion proteins (mono-AbFP)] or fused to IL-2 and IL-12 or IL-12 and GM-CSF [bifunctional fusion proteins (bi-AbFP)]. These AbFPs retained cytokine and antigen-binding activities. We have now further characterized the AbFPs and determined the heparin-binding activity of the fused cytokines, their ability to trigger IFN-gamma secretion and natural killer (NK) activation, and their direct antitumor efficacy. Flow cytometry revealed heparin-binding activity in the AbFPs containing IL-12 and IL-2, although this activity seems to be decreased in the bi-AbFPs. However, both bi-AbFPs retained the capacity to stimulate IL-12-dependent IFN-gamma secretion in the NK cell line KY-1, and IL-12/IL-2 bi-AbFP induced NK activity in splenocytes. The antitumor effectiveness of bi-AbFPs and mono-AbFP combinations was studied in mice challenged i.p. with three different human HER2/neu murine syngeneic models (D2F2/E2, CT26-HER2/neu, and MC38-HER2/neu). Although a significant variability in the profile of antitumor response was observed in the different tumor models, the combination of IL-12 and GM-CSF mono-AbFPs protected 100% of D2F2/E2-challenged and 75% of CT26-HER2/neu-challenged mice. In contrast, bi-AbFPs protected less than the combination of mono-AbFPs and, in some models, even less than mono-AbFPs alone. However, in all cases, most of long-term survivors showed protection after s.c. rechallenge with the tumors and later with the parental tumors not expressing HER2/neu. These results show that, although the pattern of protection is tumor model dependent, treatments with AbFPs can effectively generate high levels of protection against peritoneal tumors expressing HER2/neu, which may be relevant in patients with primary or metastatic peritoneal carcinomatosis that may be observed in ovarian, colon, stomach, bladder, lung, and breast cancers.
Synthesis, Characterization, and Carbon Dioxide Adsorption of Covalently Attached Polyethyleneimine-Functionalized Single-Wall Carbon Nanotubes (2008)

The reaction between fluorinated single-wall carbon nanotubes (F-SWNTs) and branched (M(w) = 600, 1800, 10000, and 25000 Da) or linear (M(w) = 25000 Da) polyethyleneimine (PEI) yields the covalent attachment of the polymer to the sidewalls of the nanotubes. The resulting PEI-functionalized SWNTs (PEI-SWNTs) were characterized by solid-state (13)C NMR, Raman spectroscopy, X-ray photoelectron spectroscopy, UV-vis spectroscopy, atomic force microscopy, transmission electron microscopy, and thermal gravimetric analysis studies. As expected, the number of polymer molecules per SWNT is larger for low molecular weight PEI than for high molecular weight PEI. However, above 1800 Da, the number of polymer molecules per SWNT does not vary as much. This is supported by Raman spectral data that shows the D:G ratio is relatively insensitive of the molecular weight for M(w) > 1800 Da. The PEI-SWNTs are shown to have solubility in aqueous media of up to 0.4 mg x mL(-1). Solid-state (13)C NMR shows the presence of carboxylate substituents that have been attributed to carbamate formation as a consequence of the reversable CO(2) absorption to the primary amine substituents of the PEI. Desorption of CO(2) is accomplished by heating under argon at 75 degrees C, while the dependence of the quantity of CO(2) absorbed on temperature and the molecular weight of the PEI is reported. Under the conditions investigated the maximum absorption of 9.2% w/w is observed for PEI(25000)-SWNT at 27 degrees C. The possible CO(2) absorption applications of the PEI-SWNTs is discussed.
Distinct Cysteine Residues in Keap1 Are Required for Keap1-Dependent Ubiquitination of Nrf2 and for Stabilization of Nrf2 by Chemopreventive Agents and Oxidative Stress (2003)

A common feature of diverse chemopreventive agents is the ability to activate expression of a genetic program that protects cells from reactive chemical species that, if left unchecked, would cause mutagenic DNA damage. The bZIP transcription factor Nrf2 has emerged as a key regulator of this cancer-preventive genetic program. Nrf2 is normally sequestered in the cytoplasm by a protein known as Keap1. Chemopreventive agents allow Nrf2 to escape from Keap1-mediated repression, although the molecular mechanism(s) responsible for activation of Nrf2 is not understood. In this report, we demonstrate that Keap1 does not passively sequester Nrf2 in the cytoplasm but actively targets Nrf2 for ubiquitination and degradation by the proteosome under basal culture conditions. We have identified two critical cysteine residues in Keap1, C273 and C288, that are required for Keap1-dependent ubiquitination of Nrf2. Both sulforaphane, a chemopreventive isothiocyanate, and oxidative stress enable Nrf2 to escape Keap1-dependent degradation, leading to stabilization of Nrf2, increased nuclear localization of Nrf2, and activation of Nrf2-dependent cancer-protective genes. We have identified a third cysteine residue in Keap1, C151, that is uniquely required for inhibition of Keap1-dependent degradation of Nrf2 by sulforaphane and oxidative stress. This cysteine residue is also required for a novel posttranslational modification to Keap1 that is induced by oxidative stress. We propose that Keap1 is a component of a novel E3 ubiquitin ligase complex that is specifically targeted for inhibition by both chemopreventive agents and oxidative stress.
Peeling Back the Layers: Controlled Erosion and Triggered Disassembly of Multilayered Polyelectrolyte Thin Films (2007)

Abstract Methods for the layer‐by‐layer deposition of oppositely charged polymers on surfaces can be used to assemble thin multilayered films using a broad range of natural, synthetic, and biologically relevant materials. These methods also permit precise, nanometer‐scale control over the compositions and internal structures of multicomponent assemblies. Provided that the individual components of these materials are selected or designed appropriately, these methods provide tantalizing new opportunities to design thin films and coatings that provide spatial, temporal, or active control over the release of one or several different agents from surfaces. The last two years have seen a significant increase in reports describing the development of new chemical, physical, and biomolecular approaches to the controlled erosion, triggered disassembly, or general deconstruction of multilayered polymer films. In this Progress Report, we highlight recent work from our laboratory and several other groups toward the design of ultrathin multilayered assemblies that i) permit broad, tunable, and sophisticated control over film erosion, and ii) provide new opportunities for the localized release of macromolecular therapeutics, such as DNA and proteins, from surfaces.