gebhart/patrepeval huggingface dataset:
The Role of Oxygen-derived Free Radicals in the Pathogenesis of Acute Pancreatitis (1984)

Acute pancreatitis may be initiated in the ex vivo, perfused canine pancreas preparation by a variety of stimuli. These include oleic acid infusion (FFA), partial duct obstruction with secretin stimulation (POSS), and a 2-hour period of ischemia (ISCH). In each model, pancreatitis is characterized by weight gain, edema, and hyperamylasemia. Oxygen-derived free radicals such as superoxide, hydrogen peroxide, and the hydroxyl radical are highly reactive toxic substances that are normally produced in small amounts during oxidative metabolism. Ordinarily, these substances are detoxified by endogenous intracellular enzymes called free radical scavengers (FRS), such as superoxide dismutase (SOD) and catalase (CAT). These studies were undertaken to evaluate the possible role of oxygen-derived free radicals in the initiation of acute pancreatitis in the isolated canine model. All preparations were perfused for 4 hours with autologous blood. Controls (N = 6): these glands remained normal in appearance, gained minimal weight (6 +/- 1 g), and serum amylase remained normal (less than 1000 u/dl). FFA pancreatitis, FFA alone (N = 6): these glands became edematous, gained weight (113.5 +/- 27.0 g), and developed hyperamylasemia (2087 +/- 387 u/dl). FFA + FRS (N = 6), SOD (50 mg) and CAT (50 mg) were added to the perfusate at time zero: these glands became only minimally edematous, gained less weight (31.8 +/- 10.1 g, p less than 0.05), and amylase remained normal (p less than 0.05). POSS pancreatitis, POSS alone (N = 8): these glands became edematous, gained weight (38.6 +/- 4.6 g), and developed marked hyperamylasemia (9522 +/- 3226 u/dl). POSS + FRS (N = 6): these glands did not develop edema, gained less weight (15.1 +/- 2.6 g, p less than 0.05), and serum amylase only increased to 1815 +/- 343 u/dl, (p less than 0.05). ISCH pancreatitis, ISCH alone (N = 6): these glands became edematous, gained weight (75.8 +/- 25 g), and developed hyperamylasemia (1679 +/- 439 u/dl). ISCH + FRS (N = 6): these glands did not develop edema, gained only 18.3 +/- 9.0 g (p less than 0.005), and serum amylase remained normal (p less than 0.05). These studies demonstrate that, in this canine preparation, acute pancreatitis is significantly ameliorated by oxygen-free radical scavengers. Since this was true whether the pancreatitis was produced by FFA infusion, POSS, or ischemia, it suggests that oxygen-derived free radicals may mediate a common essential step in the pathogenesis of all forms of pancreatitis.
Antihyperalgesic properties of the cannabinoid CT-3 in chronic neuropathic and inflammatory pain states in the rat (2005)

CT-3 (ajulemic acid) is a synthetic analogue of a metabolite of Delta9-tetrahydrocannabinol that has reported analgesic efficacy in neuropathic pain states in man. Here we show that CT-3 binds to human cannabinoid receptors in vitro, with high affinity at hCB1 (Ki 6 nM) and hCB2 (Ki 56 nM) receptors. In a functional GTP-gamma-S assay CT-3 was an agonist at both hCB1 and hCB2 receptors (EC50 11 and 13.4 nM, respectively). In behavioural models of chronic neuropathic and inflammatory pain in the rat, oral administration of CT-3 (0.1-1 mg/kg) produced up to 60% reversal of mechanical hyperalgesia. In both models the antihyperalgesic activity was prevented by the CB1-antagonist SR141716A but not the CB2-antagonist SR144528. In the tetrad of tests for CNS activity, CT-3 (1-10 mg/kg, po) produced dose-related catalepsy, deficits in locomotor performance, hypothermia, and acute analgesia. Comparison of 50% maximal effects in the tetrad and chronic pain assays produced an approximate therapeutic index of 5-10. Pharmacokinetic analysis showed that CT-3 exhibits significant but limited brain penetration, with a brain/plasma ratio of 0.4 measured following oral administration, compared to ratios of 1.0-1.9 measured following subcutaneous administration of WIN55,212-2 or Delta9-THC. These data show that CT-3 is a cannabinoid receptor agonist and is efficacious in animal models of chronic pain by activation of the CB1 receptor. Whilst it shows significant cannabinoid-like CNS activity, it exhibits a superior therapeutic index compared to other cannabinoid compounds, which may reflect a relatively reduced CNS penetration.
Addiction molecular genetics: 639,401 SNP whole genome association identifies many “cell adhesion” genes (2006)

Addictions are substantially heritable complex disorders. We now report whole genome association studies that identify 89 genes likely to contain variants that contribute to addiction vulnerability, using previously- and newly-validated microarray based pooling assays. Each gene contains clustered single nucleotide polymorphisms (SNPs) that display significant allele frequency differences between abusers and controls in each of the two samples studied with 639,401 SNP arrays and confirmatory SNPs from each of two other abuser/control samples. These genes are implicated in interesting functions, including "cell adhesion" processes that help to establish and maintain neuronal connections of special relevance to addiction's memory-like features.
Metabolic, nutritional, iatrogenic, and artifactual sources of urinary organic acids: a comprehensive table. (2002)

A comprehensive table has been designed according to organic acids and conjugates. This table is intended to assist in the interpretation of organic acid profiles because, in addition to IEM, it also refers to other pathologic causes and to physiologic, nutritional, iatrogenic, and artifactual sources. Some preanalytical issues, including possible misinterpretations, are reviewed with regard to IEM.
Data Deduplication Techniques and Analysis (2010)

Data warehouses are the repositories of data collected from several data sources, which form the backbone of most of the decision support applications. As the data sources are independent, they may adopt independent and potentially inconsistent conventions. In data warehousing applications during ETL (Extraction, Transformation and Loading) or even in OLTP (On Line Transaction Processing) applications we are often encountered with duplicate records in table. Moreover, data entry mistakes at any of these sources introduce more errors. Since high quality data is essential for gaining the confidence of users of decision support applications, ensuring high data quality is critical to the success of data warehouse implementations. Therefore, significant amount of time and money are spent on the process of detecting and correcting errors and inconsistencies. The process of cleaning dirty data is often referred to as data cleaning. To make the table data consistent and accurate we need to get rid of these duplicate records from the table. In this paper we discuss different strategies of Deduplication along with their pros and cons and some of methods used to prevent duplication in database. In addition, we have made performance evaluation with Microsoft SQL-Server 2008 on Food Mart and AdventureDB Warehouses.
Origin and evolution of the RIG-I like RNA helicase gene family (2009)

The RIG-I/MDA5 viral surveillance system is conserved in vertebrates. The RIG-I like helicase family appears to have evolved from a common ancestor that originated from genes encoding different core functional domains. Diversification of core functional domains might be fundamental to their functional divergence in terms of recognition of different viral PAMPs.
Inhibition of protoporphyrinogen oxidase expression in Arabidopsis causes a lesion‐mimic phenotype that induces systemic acquired resistance (1999)

We have used an antisense expression technology in Arabidopsis based on the yeast GAL4/UAS transactivation system (Guyer et al., Genetics, 1998; 149:633-639) to reduce levels of protoporphyrinogen IX oxidase (PPO), the last common enzyme of the biosynthesis of the haem group and chlorophyll. Plants expressing the antisense PPO gene presented growth alterations and their leaves showed necrotic lesions that appeared similar to lesions characteristic of the pathogen-induced hypersensitive reaction, and seen in the so-called lesion-mimic mutants. Plants expressing the antisense gene also had high endogenous salicylic acid levels, constitutive expression of the PR-1 gene, and were resistant to Peronospora parasitica, consistent with the activation of systemic acquired resistance (SAR). Treatment of wild-type plants with sublethal concentrations of herbicides that inhibit PPO also induced defence responses that conferred enhanced tolerance to P. parasitica. This effect was not observed in NahG and nim1 plants, which are compromised in their ability to activate SAR. These results demonstrate that genetic or chemical disruption of a metabolic pathway can lead to the induction of a set of defence responses including activation of SAR.
Overexpression of the MTA1 gene in gastrointestinal carcinomas: Correlation with invasion and metastasis (1997)

The mta1 gene is a recently identified novel candidate metastasis-associated gene. The deduced amino acid sequence contains an src homology-3 domain binding motif, a zinc finger motif and possible phosphorylation sites, suggesting that this gene is involved in signal transduction or regulation of gene expression. The purpose of our study was to examine the mRNA expression levels of the MTA1, the human homologue of the rat mta1 gene in colorectal and gastric carcinomas and thus to evaluate the relevance of the expression of this gene to human carcinoma progression. The expression of MTA1 mRNA in 36 colorectal and 34 gastric carcinoma samples was compared with that in corresponding normal mucosa tissues by semi-quantitative reverse-transcription polymerase chain reaction (RT-PCR) and the results were compared with clinico-pathologic data. A relative overexpression of MTA1 mRNA (tumor/normal ratio ≥2) was observed in 14 of 36 (38.9%) colorectal carcinomas and 13 of 34 (38.2%) gastric carcinomas. Clinico-pathologic correlations demonstrated that in colorectal carcinomas, tumors overexpressing MTA1 mRNA exhibited a significantly deeper wall invasion and a higher rate of metastasis to lymph nodes, and tended to be at an advanced Dukes' stage with frequent lymphatic involvement. In gastric carcinomas, the tumors overexpressing MTA1 mRNA showed significantly higher rates of serosal invasion and lymph node metastasis and tended to have a higher rate of vascular involvement. Our data suggest that overexpression of the MTA1 gene correlates with tumor invasion and the presence of metastases and that a high expression of MTA1 mRNA may be a potential indicator for assessing the malignant potential of colorectal and gastric carcinomas. Int. J. Cancer 74:459–463, 1997. © 1997 Wiley-Liss, Inc.
Synthesis of (E)-5-(3,3,3-trifluoro-1-propenyl)-2'-deoxyuridine and related analogs: potent and unusually selective antiviral activity of (E)-5-(3,3,3-trifluoro-1-propenyl)-2'-deoxyridine against herpes simplex virus type 1 (1984)

Syntheses of (E)-5-(3,3,3-trifluoro-1-propenyl)-2'-deoxyuridine (TFPe-dUrd) (1), 5-(3,3,3-trifluoro-1-propyl)-2'-deoxyuridine (11), 5-(3,3,3-trifluoro-1-methoxy-1-propyl)-2'-deoxyuridine (8), and 5-(3,3,3-trifluoro-1-hydroxy-1-propyl)-2'-deoxyuridine (10) from 5-chloromercuri-2'-deoxyuridine are described. The antiviral activity of TFPe-dUrd was determined in cell culture against herpes simplex virus type 1 (HSV-1), herpes simplex virus type 2 (HSV-2), and vaccinia virus and compared concurrently with 5-(1-propenyl)-2'-deoxyuridine, 5-(2-bromovinyl)-2'-deoxyuridine, 5-iodo-2'-deoxyuridine, and 5-(trifluoromethyl)-2'-deoxyuridine. TFPe-dUrd demonstrated a potent and unusually selective activity against HSV-1, with a 2-log reduction in virus yield at 0.03 micrograms/mL (0.09 microM); L-1210 cell growth was inhibited by 50% only at 290 micrograms/mL. Isopycnic centrifugation of 32P-labeled DNA indicated that if 0.5 or 2 microM TFPe-dUrd was present for 0-6 h postinfection, viral DNA synthesis was reduced by ca. 50 and 85%, respectively; concomitantly, a new DNA band appeared at lower density than normal cellular or viral DNA.
The assimilation of gamma-butyrolactone in Agrobacterium tumefaciens C58 interferes with the accumulation of the N-acyl-homoserine lactone signal. (2004)

Agrobacterium tumefaciens C58 communicates using N-acyl-homoserine lactones (acyl-HSL) and contains two lactonase-encoding genes, attM and aiiB, the products of which are capable of inactivating the acyl-HSL signal. In A. tumefaciens A6, the expression of the attKLM operon is controlled by the transcriptional repressor encoded by an adjacent gene, attJ. An attJ::Tn5 mutant does not accumulate acyl-HSL because of the constitutive expression of the lactonase AttM, the activity of which inactivates acyl-HSL. In this work, the attKLM operon of A. tumefaciens C58 was shown to be involved in an assimilative pathway of gamma-butyrolactone (GBL), gamma-hydroxybutyrate (GHB), and succinate semialdehyde (SSA), in which AttM and AttL are key enzymes for GBL and GHB assimilation. The expression of the attKLM promoter was activated in the presence of GBL, GHB, and SSA. Under these conditions, A. tumefaciens C58 did not accumulate the acyl-HSL that it naturally synthesizes, and also became able to inactivate exogenous acyl-HSL signals. Therefore, in A. tumefaciens C58, the assimilative pathway of gamma-butyrolactone interferes with the acyl-HSL signaling.
Staurosporine and ent-Staurosporine:  The First Total Syntheses, Prospects for a Regioselective Approach, and Activity Profiles1 (1996)

The total syntheses of staurosporine and ent-staurosporine have been achieved. Both glycosidic bonds were built from glycal precursors. The first was constructed by intermolecular coupling of an indole anion with a 1,2-anhydrosugar derived from an endo-glycal by direct epoxidation. The second bond was assembled from an exo-glycal by intramolecular iodoglycosylation.
Cell growth on poly(vinyl alcohol) hydrogel membranes containing biguanido groups (1994)

A cationic, high-water-content hydrogel membrane composed of poly(vinyl alcohol) (PVA) and poly(ally-biguanido-co-allylamine) hydrochloride (PAB) with positively charged biguanido groups that resemble arginine residues was developed. The PAB was prepared by reacting poly(allylamine) hydrochloride (PAA) with guanyl-O-methyl isourea. PAB/PVA hydrogel membranes were prepared by repeated freezing and thawing. For comparison, hydrogel membranes composed of PAA and PVA were also prepared. The interaction between these hydrogel membranes and mouse fibroblast (L929) was studied by a cell culture method. The PAB hydrogel blend had a relatively low percentage of initial cell attachment. The cell growth on the PAB hydrogel membranes showed a maximum at 5 mol % PAB content that was as high as commercially available plastic films. However, cells on hydrogel membranes with 50 mol % PAB content and 0 mol % PAB content (only PVA) did not seem to grow; neither did the 5/95 PAA/PVA membranes. Water contact angles of hydrogel membranes did not vary with the PAB content. Morphology of the cell attachment was observed by SEM. On the PAB blend hydrogel surfaces, cells were not spindle-shaped and monolayers, but rather cells aggregated in spherical clusters.
Alloying in Cu/Pd Nanoparticle Catalysts (1998)

In this paper we show a new application of the atomic layer epitaxy technique to prepare binary alloy nanoparticle catalysts on various supports. The technique is used to prepare Cu/Pd bimetallic catalysts on SiO2 and on γ-Al2O3. The samples were characterized by means of transmission electron microscopy (TEM) and extended X-ray absorption fine structure (EXAFS) measurements. The EXAFS results show alloying in the Cu/Pd samples with a Cu-rich surface for the alumina-supported sample and random alloying for the silica-supported sample. From TEM and EXAFS measurements the particle sizes are determined to be in the range 20−60 Å.
Improved hidden Markov modeling of phonemes for continuous speech recognition (2005)

This paper discusses the use of the Hidden Markov Model (HMM) in phonetic recognition. In particular, we present improvements that deal with the problems of modeling the effect of phonetic context and the problem of robust pdf estimation. The effect of phonetic context is taken into account by conditioning the probability density functions (pdfs) of the acoustic parameters on the adjacent phonemes, only to the extent that there are sufficient tokens of the phoneme in that context. This partial conditioning is achieved by combining the conditioned and unconditioned pdfs models with weights that depend on the confidence in each pdf estimate. This combination is shown to result in better performance than either model by itself. We also show that it is possible to obtain the computational advantages of using discrete probability densities without the usual requirement for large amounts of training data.
Blood-brain barrier: phenomenon of increasing importance to the imaging clinician (1982)

Blood-brain barrier: phenomenon of increasing importance to the imaging clinicianMR SageAudio Available | Share
In vitro activity of the antimicrobial peptide magainin 1 against Bonamia ostreae, the intrahemocytic parasite of the flat oyster Ostrea edulis. (1994)

Magainins are peptide antibiotics with broad antibacterial and antiparasitic activities, originally extracted from the skin of Xenopus laevis. We investigated the effects of magainin 1 against Bonamia ostreae, the intrahemocytic parasite of the flat oyster Ostrea edulis. Viability of purified protozoa was assessed microscopically by the uptake of the vital dyes acridine orange and ethidium bromide. Following exposure to magainin 1, Bonamia viability was reduced in a dose-dependent manner. Within the peptide concentration of 500 micrograms/ml, the parasite viability was reduced by 94%. Electron microscopy showed membrane damage and release of cytoplasmic organelles in the injured Bonamia. The study of magainin 1 activity against Ostrea edulis hemocytes did not show any morphological change in the host cells, and the peptide did not impair the capabilities of hemocytes to produce chemiluminescence when stimulated to phagocytize zymosan particles. The possibility to genetically transform molluscs to generate disease-resistant organisms is currently under investigation. Antimicrobial peptides such as magainins may provide effective gene sequences to be manipulated.
Influenza Virus A (H10N7) in Chickens and Poultry Abattoir Workers, Australia (2012)

In March 2010, an outbreak of low pathogenicity avian influenza A (H10N7) occurred on a chicken farm in Australia. After processing clinically normal birds from the farm, 7 abattoir workers reported conjunctivitis and minor upper respiratory tract symptoms. Influenza virus A subtype H10 infection was detected in 2 workers.
Controlled breathing and dyspnea in patients with chronic obstructive pulmonary disease (COPD) (2003)

Controlled breathing is included in the rehabilitation program of patients with chronic obstructive pulmonary disease (COPD). This article discusses the efficacy of controlled breathing aimed at improving dyspnea. In patients with COPD, controlled breathing works to relieve dyspnea by (1) reducing dynamic hyperinflation of the rib cage and improving gas exchange, (2) increasing strength and endurance of the respiratory muscles, and (3) optimizing the pattern of thoracoabdominal motion. Evidence of the effectiveness of controlled breathing on dyspnea is given for pursed-lips breathing, forward leaning position, and inspiratory muscle training. All interventions require careful patient selection, proper and repeated instruction, and control of the techniques and assessment of its effects. Despite the proven effectiveness of controlled breathing, several problems still need to be solved. The limited evidence of the successful transfer of controlled breathing from resting conditions to exercise conditions raises several questions: Should patients practice controlled breathing more in their daily activities? Does controlled breathing really complement the functional adaptations that patients with COPD must make? These questions need to be addressed in further research.
Proteolytic processing of the Sindbis virus membrane protein precursor PE2 is nonessential for growth in vertebrate cells but is required for efficient growth in invertebrate cells (1991)

We have shown previously that processing of the Sindbis virus envelope protein precursor PE2 to envelope protein E2 is not required for virus maturation in cultured vertebrate fibroblast cells and that unprocessed PE2 can be incorporated into infectious virus in place of E2 (J. F. Presley and D. T. Brown, J. Virol. 63:1975-1980, 1989; D. L. Russell, J. M. Dalrymple, and R. E. Johnston, J. Virol. 63:1619-1629, 1989). To better understand the role of this processing event in the invertebrate vector portion of the alphavirus life cycle, we have examined the maturation of Sindbis virus mutants defective in PE2 processing in cultured mosquito cells. We found that although substantial amounts of structural proteins PE2, E1, and C were produced in infected mosquito (aedine) cell lines, very little infectious virus was released. When the period of infection was extended, plaque size variants appeared, some of which exhibited a restored ability to grow in mosquito cells. The nucleotide sequences of two such variants were determined. These variants contained point mutations that restored PE2 cleavage, indicating a genetic linkage between failure to cleave PE2 and failure to grow in mosquito cells.
Direct and indirect effects of pulsatile shear stress on the smooth muscle cell. (2000)

Pulsatile oscillating shear stress attenuates SMC migration activity induced by EC-denve mitogens and stimulates SMC proliferative activity.
Quantitative Reverse Transcription-PCR Assay with an Internal Standard for the Detection of Prostate-specific Antigen mRNA (1999)

Abstract Background: Circulating prostate cells can be detected with a reverse transcription-PCR (RT-PCR) assay for prostate-specific antigen (PSA) mRNA. We have developed a new quantitative RT-PCR method for measuring PSA mRNA. Methods: The method uses a PSA-like internal standard (IS) mRNA that is added into the sample at the beginning of the RNA extraction and coamplified by RT-PCR with the PSA in the sample. After PCR amplification, the IS and PSA products are selectively detected by hybridization in a microtitration plate using probes labeled with fluorescent europium chelates. Results: The method was validated with PSA and IS mRNAs and PSA-expressing cells to obtain a detection limit of 50 PSA mRNA copies (i.e., signal 2 times the mean of zero signal), linearity up to 106 copies, and detection of a single PSA-expressing cell. In preliminary evaluations, 60% (n = 10) of the prostate cancer patients with skeletal metastases gave results above the detection limit (500 PSA mRNA copies in 5 mL of blood). The total number of PSA copies ranged from 900 ± 200 to 44 100 ± 4900 (mean ± SD) in the samples, corresponding to ∼1–100 PSA-expressing cells in 5 mL of blood. In the controls (n = 34), none of the healthy females and 2 of 19 healthy males had detectable PSA mRNA [700 ± 100 and 2000 ± 900 (mean ± SD) PSA mRNA copies in 5 mL of blood for the 2 males]. Conclusions: The assay provides sensitive and quantitative detection of PSA mRNA expression from blood samples and can be used to establish the clinically significant number of PSA mRNA copies in prostate cancer.