gebhart/patrepeval huggingface dataset:
Production of hydrogen peroxide by transforming growth factor-beta 1 and its involvement in induction of egr-1 in mouse osteoblastic cells. (1994)

TGF-beta 1 controls the expression of numerous genes, including early response and cellular matrix genes. However, the signal-transducing mechanism underlying this regulation of gene expression is not fully understood. In this study, we investigated whether redox regulation plays a role in the TGF-beta 1 signal transduction in the mouse osteoblastic cell line (MC3T3-E1). The overall intracellular oxidized state of the cells, when measured using 2',7'-dichlorofluorescin diacetate by laser-scanning confocal microscopy, was increased transiently after the addition of TGF-beta 1. This increase was abolished by the addition of oxygen radical scavengers such as catalase and N-acetylcysteine. In a variant cell line lacking the TGF-beta 1 receptor, the intracellular oxidized state was not modulated by treatment with TGF-beta 1. We then examined the expression of early growth response-1 (egr-1) gene, which is inducible by TGF-beta 1 and H2O2. Radical scavengers inhibited the induction of egr-1 by TGF-beta 1, but not that by 12-O-tetradecanoylphorbol-13 acetate. A nuclear run-on assay indicated that this inhibition was at the transcriptional level. From transient expression experiments using chloramphenicol acetyltransferase gene linked to serially deleted egr-1 gene 5'-upstream region, the CArG element in the 5' flanking region of egr-1 was identified as an essential sequence in the transcriptional activation for both TGF-beta 1 and H2O2 stimulation. These findings suggest that H2O2 acts as a mediator for the TGF-beta 1-induced transcription of egr-1 gene.
Near-optimal sequential testing algorithms for multiple fault isolation (2002)

In this paper, we consider the problem of constructing near-optimal test sequencing algorithms for diagnosing multiple faults. The computational complexity of solving the optimal multiple-fault isolation problem is super-exponential, that is, it is much more difficult than the single-fault isolation problem, which in itself is an NP-hard problem. Our approach is to extend the single fault sequential testing algorithms of our previous work (1990, 1991) to a class of sure strategies for diagnosing multiple faults. The proposed static diagnostic strategies are illustrated using several examples. Computational results based on real-world systems indicate that these static strategies can be used on systems with as many as 600 failure sources and 600 tests. Further, using sure strategies, an online test strategy generation program has been implemented to diagnose multiple faults in larger systems with as many as 10,000 failure sources.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Extreme Binning: Scalable, parallel deduplication for chunk-based file backup (2009)

Data deduplication is an essential and critical component of backup systems. Essential, because it reduces storage space requirements, and critical, because the performance of the entire backup operation depends on its throughput. Traditional backup workloads consist of large data streams with high locality, which existing deduplication techniques require to provide reasonable throughput. We present Extreme Binning, a scalable deduplication technique for non-traditional backup workloads that are made up of individual files with no locality among consecutive files in a given window of time. Due to lack of locality, existing techniques perform poorly on these workloads. Extreme Binning exploits file similarity instead of locality, and makes only one disk access for chunk lookup per file, which gives reasonable throughput. Multi-node backup systems built with Extreme Binning scale gracefully with the amount of input data; more backup nodes can be added to boost throughput. Each file is allocated using a stateless routing algorithm to only one node, allowing for maximum parallelization, and each backup node is autonomous with no dependency across nodes, making data management tasks robust with low overhead.
Long‐term effects of tumor necrosis factor‐α treatment on insulin signaling pathway in HepG2 cells and HepG2 cells overexpressing constitutively active Akt/PKB (2006)

Tumor necrosis factor-alpha (TNF-alpha) mediated attenuation of insulin signaling pathway is an important cause in several disorders like obesity, obesity linked diabetes mellitus. TNF-alpha actions vary depending upon concentration and time of exposure in various cells. In the present study, the effects of long-term TNF-alpha (1 ng/ml) exposure on the components of insulin signaling pathway in HepG2 and HepG2 cells overexpressing constitutively active Akt1/PKB-alpha (HepG2-CA-Akt/PKB) have been investigated. In parental HepG2 cells, TNF-alpha treatment for 24 h reduced the phosphorylation of Akt1/PKB-alpha and GSK-3beta and under these conditions cells also showed reduced insulin responsiveness in terms of Akt1/PKB-alpha and GSK-3beta phosphorylation. TNF-alpha pre-incubated HepG2-CA-Akt/PKB cells showed lower reduction in Akt1/PKB-alpha and GSK-3beta phosphorylation and insulin responsiveness after 24 h as compared to parental HepG2 cells. We report that the long-term TNF-alpha pre-incubation in both parental HepG2 and HepG2-CA-Akt/PKB-alpha cells leads to the reduction in the levels of IRS-1 without altering the levels of IRS-2. In order to understand the reason for the differential insulin resistance in both the cell types, the effect of long-term TNF-alpha treatment on the proteins upstream to Akt/PKB was investigated. TNF-alpha pre-incubation also showed reduced insulin-stimulated Tyr phosphorylation of insulin receptor (IR-beta) in both the cell types, moreover hyperphosphorylation of IRS-1 at Ser 312 residue was observed in TNF-alpha pre-incubated cells. As hyperphosphorylation of IRS-1 at Ser 312 can induce its degradation, it is possible that reduced insulin responsiveness after long-term TNF-alpha pre-incubation observed in this study is due to the decrease in IRS-1 levels.
Hypoxia aggravates lipopolysaccharide-induced lung injury (2005)

The animal model of inflammatory response induced by intratracheal application of lipopolysaccharide includes many typical features of acute lung injury or the acute respiratory distress syndrome. A number of experimental investigations have been performed to characterize the nature of this injury more effectively. In inflammatory conditions, hypoxia occurs frequently before and in parallel with pulmonary and non-pulmonary pathological events. This current study was designed to examine the in vivo effect of hypoxia as a potentially aggravating condition in endotoxin-induced lung injury. Lipopolysaccharide, 150 microg, was instilled intratracheally into rat lungs, and thereafter animals were exposed to either normoxia or hypoxia (10% oxygen). Lungs were collected 2, 4, 6 and 8 h later. Inflammatory response and tissue damage were evaluated by quantitative analysis of inflammatory cells and mediators, surfactant protein and vascular permeability. A significantly enhanced neutrophil recruitment was seen in lipopolysaccharide-animals exposed to hypoxia compared to lipopolysaccharide-animals under normoxia. This increased neutrophil accumulation was triggered by inflammatory mediators such as tumour necrosis factor-alpha and macrophage inflammatory protein-1beta, secreted by alveolar macrophages. Determination of vascular permeability and surfactant protein-B showed enhanced concentrations in lipopolysaccharide-lungs exposed to hypoxia, which was absent in animals previously alveolar macrophage-depleted. This study demonstrates that hypoxia aggravates lipopolysaccharide injury and therefore represents a second hit injury. The additional hypoxia-induced inflammatory reaction seems to be predominantly localized in the respiratory compartment, underlining the compartmentalized nature of the inflammatory response.
Bacillus subtilis alkA gene encoding inducible 3-methyladenine DNA glycosylase is adjacent to the ada operon (1993)

In Bacillus subtilis, the adaptive response to DNA alkylation depends on the ada operon, which consists of the adaA and adaB genes, which encode methylphosphotriester DNA methyltransferase (AdaA protein) and O6-methylguanine DNA methyltransferase (AdaB protein), respectively. A structural gene (alkA) that encodes 3-methyladenine DNA glycosylase was found upstream of the ada operon, but in the opposite orientation. This cluster of genes was mapped at about 235 kb from the SfiI recognition site near the origin of replication in the physical map of the B. subtilis chromosome. Disruption of the alkA gene sensitized cells to N-propyl-N'-nitro-N-nitrosoguanidine, while its overproduction rendered cells highly resistant to N-propyl-N'-nitro-N-nitrosoguanidine, indicating that lethal DNA damage produced by bulky alkylating agents was effectively counteracted by AlkA glycosylase. Transcription of the alkA gene was induced by treating adaA+ cells with methylating agents concurrent with transcription of the ada operon. This was accomplished by using methylated AdaA protein bound to a 30-bp segment in the middle of the 100-bp sequence between the transcriptional start sites of the alkA gene and ada operon. Thus, in this organism, the adaptive response to DNA alkylation is achieved by autologous activation of a divergent regulon composed of the genes for a DNA glycosylase and two species of DNA alkyltransferase.
Polyradiculoneuritis (A Case Study) (1973)

Polyradiculoneuritis (coon hound paralysis) is an ascending paralysis which occurs primarily in dogs used for hunting raccoons or in dogs which are free to roam with the opportunity of coming in contact with a raccoon. Although it is characterized by quadraplegia of the affected animal persisting for three weeks to three months, complete recovery is possible.
Cytosolic domain of the human immunodeficiency virus envelope glycoproteins binds to calmodulin and inhibits calmodulin-regulated proteins. (1993)

Calmodulin (CaM), the major intracellular receptor for calcium, is involved in regulation of diverse cellular functions. Positively charged amphipathic helical segments have been identified as an important structural motif in the recognition of CaM by different CaM-activated enzymes and peptides. The carboxyl-terminal domain of the envelope glycoproteins of human and simian immunodeficiency viruses (HIV-1, HIV-2, and SIV) contain regions that can fold into amphipathic helical segments, which closely resemble the amphipathic segments found in CaM-activated enzymes. We show here that synthetic peptide analogs corresponding to the two putative amphipathic helical regions of HIV-1/WMJ gp160 bind to CaM with high affinity (Kd 31-41 nM) in the presence of calcium. They also bind CaM in the absence of calcium, although with much lower affinity. The peptides inhibit CaM-regulated activation of bovine brain phosphodiesterase in vitro. The peptides also inhibit mitogen-induced lymphocyte activation, a property shared by CaM antagonists. Purified HIV-1 gp160 binds to CaM, while gp120, which lacks the putative amphipathic helical segments, does not bind CaM. In HIV-infected cells, the putative CaM-binding regions of gp160 are located intracellularly and may therefore interact with the cytosolic CaM. We postulate that CaM binding by HIV envelope proteins is likely to exert diverse modulatory effects, and the mechanism for HIV-induced cytotoxicity may involve, in part, inhibition of CaM-regulated cellular functions.
Characterization of High-Efficiency Cast-Si Solar Cell Wafers by MBIC Measurement (1988)

Cast-Si wafers for high-efficiency solar cells were characterized by MBIC measurement, in which the minority-carrier recombination loss at structural defects were seen as a drop in intensity. Cast-Si wafers contained a large number of non-planer and irregular grain boundaries, the majority if which had the electrical activity greatly due to a slight difference in the crystal orientation. These boundaries were classified into three geometrical structures, that is, columnar-structure grain boundary (GB), tilt-structure GB and GB structure with a transition interface layer. Other dominant defects were planar boundaries, {111} twin boundaries, {221} second-order twin boundaries and {221} planar boundaries without a twinning relationship (symmetric twist boundaries) which were found to be electrically inactive and were mainly observed in the high-quality wafers. Besides, the boundary structures off the twinning relationship, fine-crystalline structures and subgrain boundary structures were found to have remarkable electrical activity.
Limulus amoebocyte lysate assay for detection and quantitation of endotoxin in a small-volume parenteral product (1980)

A Limulus amoebocyte lysate gel-clotting method for the determination of endotoxin in a small-volume parenteral product has been described. Sample dilution with 0.1 M potassium phosphate monobasic buffer (pH 8.0) effectively eliminated assay interference, whereas dilution with water did not. The threshold pyrogenic dose for Escherichia coli EC-2 and O127:B8 endotoxins was determined to be 1.0 ng of endotoxin per kg of body weight. Not more than 1.0 ng of endotoxin (the threshold pyrogenic dose) per the highest recommended human dose or the USP pyrogen test dose per kg of body weight, whichever dose is more stringent, is a logical limit for the quantity of bacterial endotoxin in small-volume parenteral products. Excellent correlation was attained when this criterion was used to compare the Limulus amoebocyte lysate assay with the USP pyrogen test.
Budesonide and formoterol effects on rhinovirus replication and epithelial cell cytokine responses (2013)

Budesonide and formoterol can inhibit BE cell inflammatory responses in vitro without interfering with viral replication or production of interferons. These effects could potentially contribute to beneficial effects of budesonide/formoterol combination therapy in preventing RV-induced asthma exacerbations.
Adult cloning in cattle: Potential of nuclei from a permanent cell line and from primary cultures (1999)

Nuclear transfer was used to evaluate the developmental potential of nuclei from a spontaneously immortalized bovine mammary gland epithelial cell line (MECL) and from primary cultures of mammary gland cells (PMGC) and ear skin fibroblasts (PESF) established from 3-year-old cows. Cell proliferation was investigated by incorporation and detection of 5-bromo-2'-deoxyuridine (BrdU). The proportion of cells in S-phase was significantly (P < 0.05) higher for MECL cells than for PMGC and PESF, both in the presence of serum (90% vs. 28% and 15%) and following serum starvation (27% vs. 6% and 3%). Nuclei from PESF supported the development of reconstructed embryos to the blastocyst stage significantly better than those of PMGC (60% vs. 26%; P < 0.05). Embryos reconstructed with cells from MECL failed to develop to blastocysts. After transfer of embryos derived from PMGC and PESF, respectively, 2/2 and 5/12 recipients were pregnant on day 42. On day 90, the corresponding pregnancy rates were 2/2 and 3/12. One live calf derived from a PMGC was born at day 287 of gestation. Another live PESF-derived calf was delivered by caesarean section at day 286 of gestation. Our study suggests that nuclei from primary cultures of adult cells can be successfully reprogrammed by nuclear transfer, whereas nuclei from a permanent cell line failed to support the development of nuclear transfer embryos.
Phase‐shift, stimuli‐responsive perfluorocarbon nanodroplets for drug delivery to cancer (2012)

This review focuses on phase-shift perfluorocarbon nanoemulsions whose action depends on an ultrasound-triggered phase shift from a liquid to gas state. For drug-loaded perfluorocarbon nanoemulsions, microbubbles are formed under the action of tumor-directed ultrasound and drug is released locally into tumor volume in this process. This review covers in detail mechanisms involved in the droplet-to-bubble transition as well as mechanisms of ultrasound-mediated drug delivery.
Therapeutic applications of fenugreek. (2003)

Fenugreek has a long history of medical uses in Ayurvedic and Chinese medicine, and has been used for numerous indications, including labor induction, aiding digestion, and as a general tonic to improve metabolism and health. Preliminary animal and human trials suggest possible hypoglycemic and antihyperlipidemic properties of oral fenugreek seed powder.
The Effects of an Interspinous Implant on Intervertebral Disc Pressures (2003)

The implant does not significantly change the intradiscal pressures at the adjacent levels, yet it significantly unloads the intervertebral disc at the instrumented level in the neutral and extended positions. On the basis of the current findings, it does not appear that the implant causes accelerated disc degeneration at the adjacent levels.
A Molecular Mechanism for Human T-cell Leukemia Virus Latency and Tax Transactivation (1995)

The human T-cell leukemia virus type I (HTLV-I) is the causative agent of an aggressive T-cell malignancy in humans. While the virus appears to maintain a state of latency in most infected cells, high level virion production is an essential step in the HTLV-I life cycle. The virally-encoded Tax protein, a potent activator of gene expression, is believed to control the switch from latency to replication. Tax stimulation of HTLV-I transcription is mediated through cellular activating transcription factor/cAMP response element binding proteins, which bind the three 21-base pair (bp) repeat viral enhancer elements. In this report, we show that viral latency may result from a highly unstable interaction between CREB and the HTLV-I 21-bp repeats, resulting in rapid dissociation of CREB from the viral promoter. In the presence Tax, the dissociation rate of CREB from a 21-bp repeat element is decreased. This stabilization is highly specific, requiring the amino-terminal region of CREB and appropriate 21-bp repeat sequences. We suggest that Tax stabilization of CREB binding to the viral promoter leads to an increase in gene expression, possibly providing the switch from latency to high level replication of the virus.
RETRACTED: Activation of the NF-κB pathway by adeno-associated virus (AAV) vectors and its implications in immune response and gene therapy (2011)

Because our in silico analysis with a human transcription factor database demonstrated the presence of several binding sites for NF-κB, a central regulator of cellular immune and inflammatory responses, in the adeno-associated virus (AAV) genome, we investigated whether AAV uses NF-κB during its life cycle. We used small molecule modulators of NF-κB in HeLa cells transduced with recombinant AAV vectors. VP16, an NF-κB activator, augmented AAV vector-mediated transgene expression up to 25-fold. Of the two NF-κB inhibitors, Bay11, which blocks both the canonical and the alternative NF-κB pathways, totally ablated transgene expression, whereas pyrrolidone dithiocarbamate, which interferes with the classical NF-κB pathway, had no effect. Western blot analyses confirmed the abundance of the nuclear p52 protein component of the alternative NF-κB pathway in the presence of VP16, which was ablated by Bay11, suggesting that AAV transduction activates the alternative NF-κB pathway. In vivo, hepatic AAV gene transfer activated the canonical NF-κB pathway within 2 h, resulting in expression of proinflammatory cytokines and chemokines (likely reflecting the sensing of viral particles by antigen-presenting cells), whereas the alternative pathway was activated by 9 h. Bay11 effectively blocked activation of both pathways without interfering with long-term transgene expression while eliminating proinflammatory cytokine expression. These studies suggest that transient immunosuppression with NF-κB inhibitors before transduction with AAV vectors should lead to a dampened immune response, which has significant implications in the optimal use of AAV vectors in human gene therapy.
Secreted Heat Shock Protein 90α Induces Colorectal Cancer Cell Invasion through CD91/LRP-1 and NF-κB-mediated Integrin αV Expression (2010)

HCT-8 colon cancer cells secreted heat shock protein 90alpha (HSP90alpha) and had increased invasiveness upon serum starvation. The concentrated conditioned medium of serum-starved HCT-8 cells was able to stimulate the migration and invasion of non-serum-starved cells, which could be prevented by treatment with an anti-HSP90alpha antibody. Recombinant HSP90alpha (rHSP90alpha) also enhanced HCT-8 cell migration and invasion, suggesting a stimulatory role of secreted HSP90alpha in cancer malignancy. HSP90alpha binding to CD91alpha and Neu was evidenced by the proximity ligation assay, and rHSP90alpha-induced HCT-8 cell invasion could be suppressed by the addition of anti-CD91alpha or anti-Neu antibodies. Via CD91alpha and Neu, rHSP90alpha selectively induced integrin alpha(V) expression, and knockdown of integrin alpha(V) efficiently blocked rHSP90alpha-induced HCT-8 cell invasion. rHSP90alpha induced the activities of ERK, PI3K/Akt, and NF-kappaB p65, but only NF-kappaB activation was involved in HSP90alpha-induced integrin alpha(V) expression. Additionally, we investigated the serum levels of HSP90alpha and the expression status of tumor integrin alpha(V) mRNA in colorectal cancer patients. Serum HSP90alpha levels of colorectal cancer patients were significantly higher than those of normal volunteers (p < 0.001). Patients with higher serum HSP90alpha levels significantly exhibited elevated levels of integrin alpha(V) mRNA in tumor tissues as compared with adjacent non-tumor tissues (p < 0.001). Furthermore, tumor integrin alpha(V) overexpression was significantly correlated with TNM (Tumor, Node, Metastasis) staging (p = 0.001).
Analysis of Nucleic Acids by Capillary Electrophoresis (1997)

Part 1: Basic Concepts Separation Matrix - Electrophoresis theories - Microscopic studies Part 2: Factors affecting the separation Electric field and polymer concentration - Sample matrix and injection - Agglomeration Part 3: Development in instrumentation Pulsed field CE - New type of separation matrix - Blotting - DNA separation Part 4: Applications Separation of restriction fragments - Analysis of oligonucleotides - DNA sequencing - Antisense DNA - Mutational analysis