gebhart/patrepeval huggingface dataset:
Making the Most of the Internet for Failure Analysis (1998)

Abstract The growth of the Internet over the past four years provides the failure analyst with a new media for communicating his results. The new digital media offers significant advantages over analog publication of results. Digital production, distribution and storage of failure analysis results reduces copying costs and paper storage, and enhances the ability to search through old analyses. When published digitally, results reach the customer within minutes of finishing the report. Furthermore, images on the computer screen can be of significantly higher quality than images reproduced on paper. The advantages of the digital medium come at a price, however. Research has shown that employees can become less productive when replacing their analog methodologies with digital methodologies. Today's feature-filled software encourages "futzing," one cause of the productivity reduction. In addition, the quality of the images and ability to search the text can be compromised if the software or the analyst does not understand this digital medium. This paper describes a system that offers complete digital production, distribution and storage of failure analysis reports on the Internet. By design, this system reduces the futzing factor, enhances the ability to search the reports, and optimizes images for display on computer monitors. Because photographic images are so important to failure analysis, some digital image optimization theory is reviewed.
Inactivation of HDAC5 by SIK1 in AICAR-treated C2C12 Myoblasts (2009)

Salt inducible kinase (SIK) 1, a member of the AMP-activated kinase (AMPK) family, is activated by the AMPK-activator LKB1 which phosphorylates SIK1 at Thr182. The activated SIK1 then auto-phosphorylates its Ser186 located at the +4 position of Thr182. The phospho-Ser186 is essential for sustained activity of SIK1, which is maintained by sequential phosphorylation at Ser186-Thr182 by glycogen synthase kinase (GSK)-3beta. Meanwhile, SIK1 represses the transcription factor cAMP-response element binding protein (CREB) by phosphorylating its co-activator transducer of regulated CREB activity (TORC). Recently, histone deacetylase (HDAC) 5 was identified as a new substrate of SIK1. Inhibition of SIK1 or AMPK results in the stimulation of glyconeogensis in the liver by enhancing dephosphorylation of TORC2 followed by up-regulation of peroxisome proliferator-activated receptor coactivator (PGC)-1alpha gene expression. However, expression of the PGC-1alpha gene has been found to be repressed in LKB1-defective muscle cells. Our findings show that the AMPK agonist 5-aminoimidazole-4-carboxamide-1-beta-d-ribofuranoside (AICAR)-dependent expression of PGC-1alpha is diminished by inhibitors of GSK-3beta or SIKs in C2C12 myoblasts. Treatment with AICAR or the overexpression of SIK1 induces nuclear export of HDAC5 followed by the activation of myogenic transcription factor (MEF)-2C. The levels of phosphorylation at Thr182 and Ser186 of SIK1 in AICAR-treated C2C12 cells are elevated, and GSK-3beta enzyme purified from AICAR-treated cells shows enhanced phosphorylation activity of SIK1 in vitro. These observations suggest that GSK-3 beta and SIK1 may play important roles in the regulation of PGC-1alpha gene expression by inactivating HDAC5 followed by activation of MEF2C.
Recombinant and in vitro RNA synthesis : methods and protocols (2012)

The discovery of catalytic RNAs in the mid-1980s marked the beginning of a new era in RNA biology and an ever increasing appreciation of the diverse and critical roles played by this fascinating molecule. In Recombinant and In Vitro RNA Synthesis: Methods and Protocols, expert researchers in the field detail approaches from the inception of a new RNA project to the final sample ready for analysis. These experimental protocols combine established work-horse approaches with some of the latest innovative methods for RNA synthesis and purification. Written in the highly successful Methods in Molecular Biology™ series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Recombinant and In Vitro RNA Synthesis: Methods and Protocols aids scientists in continuing to study the fascinating world of RNA.
Transcriptional Regulation of Squalene Epoxidase by Sterols and Inhibitors in HeLa Cells (1996)

Regulation of squalene epoxidase (SE) gene expression was studied in comparison with those of 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) reductase and low density lipoprotein (LDL) receptor. An increased expression of SE mRNA and protein content in mouse L929 cells grown in 10% lipoprotein-deficient fetal bovine serum (LPDS) for 48 h was found by performing immunoblot and Northern blot analyses when compared with the culture in the presence of fetal bovine serum (FBS). The same results in mRNA levels were seen using human cell lines HepG2, HeLa, and Chang liver cells. The increase of SE mRNA in HeLa cells grown in LPDS was preventable in a dose-dependent manner by feeding cells with 25-hydroxycholesterol or cholesterol. When an SE inhibitor, NB-598, was fed to HeLa cells grown in LPDS, it caused further increases in mRNA levels of SE, HMG-CoA reductase, and LDL receptor. In contrast, NB-598 had no effect on the message levels of these genes when fed to HeLa cells grown in FBS. These results suggest that sterol produced endogenously can also regulate SE expression at the level of transcription.
Synthesis and Evaluation of a Peptide Targeted Small Molecular Gd-DOTA Monoamide Conjugate for MR Molecular Imaging of Prostate Cancer (2012)

Tumor extracellular matrix has an abundance of cancer related proteins that can be used as biomarkers for cancer molecular imaging. Innovative design and development of safe and effective targeted contrast agents to these biomarkers would allow effective MR cancer molecular imaging with high spatial resolution. In this study, we synthesized a low molecular weight CLT1 peptide targeted Gd(III) chelate CLT1-dL-(Gd-DOTA)(4) specific to clotted plasma proteins in tumor stroma for cancer MR molecular imaging. CLT1-dL-(Gd-DOTA)(4) was synthesized by conjugating four Gd-DOTA monoamide chelates to a CLT1 peptide via generation 1 lysine dendrimer. The T(1) relaxivity of CLT1-dL-(Gd-DOTA)(4) was 40.4 mM(-1) s(-1) per molecule (10.1 mM(-1) s(-1) per Gd) at 37 °C and 1.5 T. Fluorescence imaging showed high binding specificity of CLT1 to orthotopic PC3 prostate tumor in mice. The contrast agent resulted in improved tumor contrast enhancement in male athymic nude mice bearing orthotopic PC3 prostate tumor xenograft at a dose of 0.03 mmol Gd/kg. The peptide targeted MRI contrast agent is promising for high-resolution MR molecular imaging of prostate tumor.
Confirmation study of prostate cancer risk variants at 8q24 in African Americans identifies a novel risk locus (2007)

Prostate cancer is a common complex disease that disproportionately affects men of African descent. Recently, several different common variants on chromosome 8q24 have been shown to be associated with prostate cancer in multiple studies and ethnic groups. The objective of this study was to confirm the association of 8q24 markers with prostate cancer in African Americans. We genotyped 24 markers along 8q24 and 80 unlinked ancestry informative markers in a hospital-based case-control sample of 1057 African American men (490 prostate cancer cases and 567 controls). Association analyses of 8q24 markers with prostate cancer risk were adjusted for both global and local 8q24 admixture stratification using estimates from ancestry informative markers. We report that rs7008482, which maps to the 8q24.13 region, is an additional independent prostate cancer risk variant (P = 5 x 10(-4)), and we also replicate the association of rs16901979 with prostate cancer (P = 0.002). Other published risk variants in the region such as rs1447295 and rs6983267 showed a similar direction and magnitude of effect, but were not significant in our population. Both rs7008482 and rs16901979 independently predicted risk and remained significant (P < 0.001) after controlling for each other. Our data combined with additional replications of 8q24 markers provide compelling support for multiple regions of risk for prostate cancer on 8q24.
MANNHEIMIA (PASTEURELLA) HAEMOLYTICA LEUKOTOXIN UTILIZES CD18 AS ITS RECEPTOR ON BIGHORN SHEEP LEUKOCYTES (2007)

Pneumonia caused by Mannheimia (Pasteurella) haemolytica is a highly fatal disease of bighorn sheep (Ovis canadensis). Leukotoxin (Lkt), secreted by M. haemolytica, is an important virulence factor of this organism, and is cytolytic to bighorn sheep leukocytes. Previously, we have shown that CD18, the beta subunit of beta2 integrins, serves as the receptor for Lkt on bovine leukocytes. Furthermore, anti-CD18 antibodies inhibit Lkt-induced cytotoxicity of bighorn sheep leukocytes. Therefore, we hypothesized that Lkt utilizes CD18 as its receptor on bighorn sheep leukocytes. Confirmation of bighorn sheep CD18 as a receptor for Lkt requires the demonstration that the recombinant expression of bighorn sheep CD18 in Lkt-nonsusceptible cells renders them susceptible to Lkt. Therefore, we transfected cDNA encoding CD18 of bighorn sheep into a Lkt-nonsusceptible murine cell line. Cell surface expression of bighorn sheep CD18 on the transfectants was tested by flow cytometry with anti-CD18 antibodies. Transfectants stably expressing bighorn sheep CD18 on their surface were subjected to flow cytometric analysis for detection of Lkt binding, and cytotoxicity assays for detection of Lkt-induced cytotoxicity. Leukotoxin bound to the transfectants. More importantly, the transfectants were effectively lysed by Lkt in a concentration-dependent manner, whereas the parent cells were not. These results clearly indicate that M. haemolytica Lkt utilizes CD18 as a receptor on bighorn sheep leukocytes. Identification of CD18 as a receptor for Lkt on bighorn sheep leukocytes should enhance our understanding of the pathogenesis of pneumonia, which in turn should help in the development of control measures against this fatal disease of bighorn sheep.
Synergistic Catalysis over Bimetallic Alloy Nanoparticles (2013)

Abstract Bimetallic nanoparticles (NPs) have emerged as an important class of catalysts. In many cases, bimetallic alloy NPs have higher catalytic efficiencies than their monometallic counterparts, owing to strong synergy between the metals. In this Review, we survey the research progress on the synergistic effect of bimetallic alloy NPs for catalytic reactions related to fuel cells, such as the electrochemical oxidation of MeOH, EtOH, and formic acid, CO oxidation, the oxygen‐reduction reaction, and the dehydrogenation of ammonia borane, formic acid, hydrous hydrazine, hydrazine borane, etc. In addition, the use of synergistic catalysis in some other important reactions has also been reviewed. Recent developments in synergistic catalysis over bimetallic alloy NPs will provide access to a variety of low‐cost and high‐performance catalysts for laboratory and industrial applications within the next few years.
Effect of Enzyme Supplementation on the Nutritional Value of Raw, Autoclaved, and Dehulled Lupins (Lupinus albus) in Chicken Diets (1993)

The effects of adding crude enzyme preparations to diets containing raw, autoclaved, and dehulled lupin seeds on the performance of broiler and Leghorn chicks (7 to 21 days) were evaluated in five experiments. In the first experiment, enzyme addition (combination of Energex-carbohydrase, Bio-Feed Pro-protease, and Novozyme-alpha-galactosidase) to a diet containing 70% raw lupins improved the weight gain and feed to gain ratio of broiler chicks by 18 and 10%, respectively. The relative intestinal length and gizzard weight also were reduced by enzyme treatment. In the second experiment, the optimum concentration of enzymes was determined in diets containing 50% raw lupins. Bio-Feed Pro at 3% increased weight gains by 24% and the feed to gain ratio by 11%, whereas a combination of three enzymes at .10% of each yielded respective improvements of 18 and 9%. In Experiment 3, the AME and protein digestibility of dehulled lupin seeds were increased by 18 and 7% compared with those for raw seeds. Autoclaving (20 min) significantly (P < .05) improved chick performance and AME and protein digestibility of raw seeds. In the fourth experiment, autoclaving (15 min), dehulling, and a combination of both improved weight gains by 11, 15, and 8% and feed to gain ratios by 4, 11, and 6%, respectively. Enzyme addition improved the performance of birds fed raw, but not autoclaved lupin diets. In the fifth experiment, dehulling and enzyme treatment but not autoclaving (20 min) improved the performance of birds fed diets containing 50% lupins. The relative weight of gizzard was reduced by both treatments but that of the pancreas was affected only by enzyme treatment. Overall, enzyme supplementation of raw lupin diets considerably improved chick performance. Dehulling of lupins also improved chick performance with results for autoclaved lupins being inconsistent.
Thromboxane A2 is a mediator of cyclooxygenase-2-dependent endothelial migration and angiogenesis. (1999)

Cyclooxygenase-2 (COX-2) inhibitors reduce angiogenic responses to a variety of stimuli, suggesting that products of COX-2 may mediate critical steps. Here, we show that thromboxane A2 (TXA2) is one of several eicosanoid products generated by activated human microvascular endothelial cells. Selective COX-2 antagonists inhibit TXA2 production, endothelial migration, and fibroblast growth factor-induced corneal angiogenesis. Endothelial migration and corneal angiogenesis are similarly inhibited by a TXA2 receptor antagonist, SQ29548. A TXA2 agonist, U46619, reconstitutes both migration and angiogenesis responses under COX-2-inhibited conditions. These findings identify TXA2 as a COX-2 product that functions as a critical intermediary of angiogenesis.
Repair of human articular cartilage after implantation of autologous chondrocytes (1999)

Tissue engineering is an increasingly popular method of addressing pathological disorders of cartilage. Recent studies have demonstrated its clinical efficacy, but there is little information on the structural organisation and biochemical composition of the repair tissue and its relation to the adjacent normal tissue. We therefore analysed by polarised light microscopy and immunohistochemistry biopsies of repair tissue which had been taken 12 months after implantation of autologous chondrocytes in two patients with defects of articular cartilage. Our findings showed zonal heterogeneity throughout the repair tissue. The deeper zone resembled hyaline-like articular cartilage whereas the upper zone was more fibrocartilaginous. The results indicate that within 12 months autologous chondrocyte implantation successfully produces replacement cartilage tissue, a major part of which resembles normal hyaline cartilage.
Overexpression of the Wilms' tumor gene WT1 in head and neck squamous cell carcinoma (2003)

The expression levels of the Wilms' tumor gene WT1 were examined in 56 cases of head and neck squamous cell carcinoma (HNSCC) using quantitative real-time reverse transcriptase-polymerase chain reaction (RT-PCR). They included 4 cases of floor of mouth, 9 of gingiva, 25 of tongue, 10 of oropharynx, 3 of hypopharynx, and 5 larynx squamous cell carcinoma (SCC). All (100%) of 4 cases of floor of mouth, 5 (56%) of 9 gingiva, 17 (68%) of 25 tongue, 8 (80%) of 10 oropharynx, all (100%) of 3 hypopharynx, and all (100%) of 5 larynx SCC overexpressed the WT1 gene in the range of 3.07 x 10(-4)-8.60 x 10(-1) levels (the WT1 expression level in K562 leukemic cells was defined as 1.0). Thus, 42 (75%) out of 56 cases of HNSCC overexpressed the WT1 gene. The high expression level of the WT1 gene significantly correlated with poor histological tumor differentiation and high tumor stage of HNSCC. Immunohistochemical analysis confirmed the expression of WT1 protein in 6 cases (one floor of mouth, 2 tongue, 2 oropharynx, and one larynx SCC) with overexpression of the WT1 gene. The direct sequencing analysis of the WT1 genomic DNA showed no mutations in any of 10 exons of the WT1 gene in 5 different HNSCC. These findings suggest an important role of the wild-type WT1 gene in the tumorigenesis of HNSCC.
Topic models with power-law using Pitman-Yor process (2010)

One important approach for knowledge discovery and data mining is to estimate unobserved variables because latent variables can indicate hidden specific properties of observed data. The latent factor model assumes that each item in a record has a latent factor; the co-occurrence of items can then be modeled by latent factors. In document modeling, a record indicates a document represented as a "bag of words," meaning that the order of words is ignored, an item indicates a word and a latent factor indicates a topic. Latent Dirichlet allocation (LDA) is a widely used Bayesian topic model applying the Dirichlet distribution over the latent topic distribution of a document having multiple topics. LDA assumes that latent topics, i.e., discrete latent variables, are distributed according to a multinomial distribution whose parameters are generated from the Dirichlet distribution. LDA also models a word distribution by using a multinomial distribution whose parameters follows the Dirichlet distribution. This Dirichlet-multinomial setting, however, cannot capture the power-law phenomenon of a word distribution, which is known as Zipf's law in linguistics. We therefore propose a novel topic model using the Pitman-Yor(PY) process, called the PY topic model. The PY topic model captures two properties of a document; a power-law word distribution and the presence of multiple topics. In an experiment using real data, this model outperformed LDA in document modeling in terms of perplexity.
Contrasting activity of cytosin–guanosin dinucleotide oligonucleotides in mice with experimental colitis (2003)

Intestinal inflammation in inflammatory bowel disease (IBD) and experimental models of colitis is characterized by a dysregulated intestinal immune response with elevated levels of Th1 cytokines. The luminal flora has been implicated as a major factor contributing to the initiation and perpetuation of inflammation in experimental colitis by mechanisms not known. Bacterial DNA contains unmethylated cytosin-guanosin dinucleotides (CpG) which strongly activate Th1-mediated immune responses. To test whether these CpG-motifs modulate intestinal inflammation we treated mice with dextran sulphate sodium (DSS)-induced colitis with CpG-containing oligodeoxynucleotides (CpG-ODN). CpG-ODN given after the onset of DSS colitis aggravated the disease, as indicated by a significantly increased loss of body weight and a 30% increase of the histological score. Further, we found a severe increase of proinflammatory cytokines (interleukin (IL)-6: 40-fold; interferon (IFN)-gamma: 11-fold). In a pretreatment setting CpG-ODN reduced weight loss significantly and reduced intestinal inflammation by 45%. Colonic IFN-gamma and IL-6 mRNA levels were reduced by 75%, and IL-10 was elevated by 400% compared to controls. The prophylactic CpG-effect was not imitated by IL-12 because IL-12 pretreatment was not protective. In time-course experiments, CpG-ODN pretreatment over 5 days resulted in a tolerance effect concerning its IFN-gamma-inducing quality, and during the following days of colitis induction IL-10 secretion from mesenterial lymph node cells was elevated compared to controls. Therefore, the prophylactic effect of CpG-ODN might be explained by its tolerizing effect and/or the increased ability for IL-10 production during the consecutive intestinal inflammation.
Increased tissue factor activity of monocytes/macrophages isolated from canine renal allografts (1984)

Kidney allografting was performed in a group of ten beagles, and viable leukocytes infiltrating the transplanted organs were isolated during episodes of acute rejection 5 or 6 days postoperatively. These infiltrate populations, consisting predominantly of lymphocytes and monocytes/macrophages, were found to have significantly increased amounts of procoagulant activity relative to control leukocytes isolated from circulating blood and lymph. Using nonspecific esterase staining in an agar microclot assay, procoagulant activity in the infiltrate leukocytes was found to reside in monocytes/macrophages rather than other coisolated cell types. By contrast, control monocytes from blood had no activity in this microclot assay. Procoagulant activity in the infiltrate cells was characterized as tissue factor. Increased amounts of this activator of the extrinsic pathway, as found in infiltrate monocytes/macrophages, may initiate clotting reactions and fibrin deposition within allografts.
A human Cds1-related kinase that functions downstream of ATM protein in the cellular response to DNA damage (1999)

Checkpoints maintain the order and fidelity of the eukaryotic cell cycle, and defects in checkpoints contribute to genetic instability and cancer. Much of our current understanding of checkpoints comes from genetic studies conducted in yeast. In the fission yeast Schizosaccharomyces pombe (Sp), SpRad3 is an essential component of both the DNA damage and DNA replication checkpoints. The SpChk1 and SpCds1 protein kinases function downstream of SpRad3. SpChk1 is an effector of the DNA damage checkpoint and, in the absence of SpCds1, serves an essential function in the DNA replication checkpoint. SpCds1 functions in the DNA replication checkpoint and in the S phase DNA damage checkpoint. Human homologs of both SpRad3 and SpChk1 but not SpCds1 have been identified. Here we report the identification of a human cDNA encoding a protein (designated HuCds1) that shares sequence, structural, and functional similarity to SpCds1. HuCds1 was modified by phosphorylation and activated in response to ionizing radiation. It was also modified in response to hydroxyurea treatment. Functional ATM protein was required for HuCds1 modification after ionizing radiation but not after hydroxyurea treatment. Like its fission yeast counterpart, human Cds1 phosphorylated Cdc25C to promote the binding of 14-3-3 proteins. These findings suggest that the checkpoint function of HuCds1 is conserved in yeast and mammals.
A Colour Atlas of Endodontics (1988)

Radiography histology of the pulp diagnosis and treatment planning anaesthesia basic instruments and materials rubber dam treatment of the emergency patient access cavities root canal anatomy preparation of the tooth preparation of the root canal filling the root canal calcium hydroxide primary dentition surgical endodontics endo perio lesion root resorption removal of root canal obstructions bleaching restoration of the treated tooth the way ahead.
Stability and performance analysis of pitch filters in speech coders (1987)

This paper analyzes the stability and performance of pitch filters in speech coding when pitch prediction is combined with formant prediction. A computationally simple stability test based on a sufficient condition is formulated for pitch synthesis filters. For typical orders of pitch filters, this sufficient test is very tight. Based on the test, a simple stabilization technique that minimizes the loss in prediction gain of the pitch predictor is employed to generate stable synthesis filters. Finally, it is observed that the quality of decoded speech improves significantly when stable synthesis filters are employed.