gebhart/patrepeval huggingface dataset:
Functional Compartmentation of dCTP Pools (1995)

The utilization of dCTP derived from de novo synthesis through ribonucleotide reductase in exponentially growing CCRF-CEM cells was compared with the metabolic fate of dCTP produced by the salvage pathway. Exogenous dCyd was not effectively incorporated into replicating DNA; instead, dCTP derived from ribonucleotide reductase (labeled by [5-3H]Cyd) was the main precursor for that purpose, apparently because of functional compartmentation of the dCTP pool in these cells. Studies of the metabolic route of incorporation of exogenous [5-3H]dCyd into DNA of growing CCRF-CEM cells demonstrated that it was mainly incorporated through the DNA repair pathway. Incorporation of [5-3H]dCyd into DNA of synchronized cell populations was maximal in G1 cells, whereas [3H]dThd incorporation occurred predominantly in S phase cells. When cellular DNA was density labeled by incubation with BrdUrd, repaired DNA, which was less dense than replicated DNA, was preferentially labeled by [5-3H]dCyd. In contrast, replicated DNA was labeled by both [3H]dThd and [5-3H]Cyd. The DNA-damaging agents methylmethanesulfonate, ultraviolet irradiation, and gamma-irradiation inhibited [3H]dThd incorporation, whereas they stimulated the accumulation of [5-3H]dCyd in DNA. Based on these results, we propose that the dCTP pool is functionally compartmentalized in growing CCRF-CEM cells. dCTP derived from the salvage pathway is utilized predominantly for DNA repair, whereas the de novo pathway supplies dCTP for DNA replication.
Quorum sensing in Aeromonas hydrophila and Aeromonas salmonicida: identification of the LuxRI homologs AhyRI and AsaRI and their cognate N-acylhomoserine lactone signal molecules (1997)

Spent culture supernatants from both Aeromonas hydrophila and Aeromonas salmonicida activate a range of biosensors responsive to N-acylhomoserine lactones (AHLs). The genes for a quorum sensing signal generator and a response regulator were cloned from each Aeromonas species and termed ahyRI and asaRI, respectively. Protein sequence homology analysis places the gene products within the growing family of LuxRI homologs. ahyR and asaR are transcribed divergently from ahyI and asaI, respectively, and in both Aeromonas species, the genes downstream have been identified by DNA sequence and PCR analysis. Downstream of both ahyI and asaI is a gene with close homology to iciA, an inhibitor of chromosome replication in Escherichia coli, a finding which implies that in Aeromonas, cell division may be linked to quorum sensing. The major signal molecule synthesized via both AhyI and AsaI was purified from spent culture supernatants and identified as N-(butanoyl)-L-homoserine lactone (BHL) by thin-layer chromatography, high-pressure liquid chromatography analysis, and mass spectrometry. In addition, a second, minor AHL, N-hexanoyl-L-homoserine lactone, was identified. Transcriptional reporter studies with ahyI::luxCDABE fusions indicate that AhyR and BHL are both required for ahyI transcription. For A. salmonicida, although the addition of exogenous BHL gives only a small stimulation of the production of serine protease with comparison to the control culture, the incorporation of a longer-chain AHL, N-(3-oxodecanoyl)-L-homoserine lactone, reduced the final level (by approximately 50%) and delayed the appearance (from an A650 of 0.9 in the control to an A650 of 1.2 in the test) of protease in the culture supernatant. These data add A. hydrophila and A. salmonicida to the growing family of gram-negative bacteria now known to control gene expression through quorum sensing.
Enterohemorrhagic Escherichia coli Specific Enterohemolysin Induced IL-1β in Human Macrophages and EHEC-Induced IL-1β Required Activation of NLRP3 Inflammasome (2012)

Enterohemorrhagic Escherichia coli (EHEC) O157:H7 is a major foodborne pathogen causing hemorrhagic colitis and hemolytic-uremic syndrome. The role of EHEC O157:H7-enterohemolysin (Ehx) in the pathogenesis of infections remains poorly defined. In this study, we used gene deletion and complement methods to confirm its putative functions. Results demonstrated that, in THP-1 cells, EHEC O157:H7-Ehx is associated with greater production of extracellular interleukin (IL)-1β than other cytokines. The data also showed that EHEC O157:H7-Ehx contributed to cytotoxicity in THP-1 cells, causing the release of lactate dehydrogenase (LDH). Although we observed a positive correlation between IL-1β production and cytotoxicity in THP-1 cells infected with different EHEC O157:H7 strains, our immunoblot results showed that the majority of IL-1β in the supernatant was mature IL-1β and not the pro-IL-1β that can be released after cell death. However, EHEC O157:H7-Ehx had no detectable effect on biologically inactive pro-IL-1β at the mRNA or protein synthesis levels. Neither did it affect the expression of apoptosis-associated speck-like protein containing a CARD (ASC), caspase-1, or NOD-like receptor family pyrin domain containing 3 (NLRP3). RNA interference experiments showed that EHEC O157:H7-induced IL-1β production required the involvement of ASC, caspase-1, and NLRP3 expression in THP-1 cells. Our results demonstrate that Ehx plays a crucial role in EHEC O157:H7-induced IL-1β production and its cytotoxicity to THP-1 cells. NLRP3 inflammasome activation is also involved in EHEC O157:H7-stimulated IL-1β release.
Particular object retrieval with integral max-pooling of CNN activations (2015)

Recently, image representation built upon Convolutional Neural Network (CNN) has been shown to provide effective descriptors for image search, outperforming pre-CNN features as short-vector representations. Yet such models are not compatible with geometry-aware re-ranking methods and still outperformed, on some particular object retrieval benchmarks, by traditional image search systems relying on precise descriptor matching, geometric re-ranking, or query expansion. This work revisits both retrieval stages, namely initial search and re-ranking, by employing the same primitive information derived from the CNN. We build compact feature vectors that encode several image regions without the need to feed multiple inputs to the network. Furthermore, we extend integral images to handle max-pooling on convolutional layer activations, allowing us to efficiently localize matching objects. The resulting bounding box is finally used for image re-ranking. As a result, this paper significantly improves existing CNN-based recognition pipeline: We report for the first time results competing with traditional methods on the challenging Oxford5k and Paris6k datasets.
Synthetic Peptides for Production of Antibodies that Recognize Intact Proteins (2002)

Antibodies that recognize intact proteins can be produced through the use of synthetic peptides based on short stretches of the protein sequence, without first having to isolate the protein. The procedure for selecting the antigenic sequence is relatively straightforward. This unit identifies ways to determine the best sequence and to chemically couple the synthetic peptide to a carrier protein to boost the immune response. Another method entails direct synthesis of a MAP covalent multimer of the simple peptide sequence. Peptides can also be coupled to carrier proteins through either their amino or carboxyl groups. Alternate protocols in this unit cover these scenarios. In addition, methods for assaying free sulfhydryl content and for reducing disulfide bonds in synthetic peptides are provided. Finally, once the coupling procedure has been performed, it is possible to determine the approximate degree of coupling by amino acid analysis, and a procedure for this is also provided.
IMMUNOHISTOCHEMICAL LOSS OF THYROID PEROXIDASE IN PAPILLARY THYROID CARCINOMA: STRONG SUPPRESSION OF PEROXIDASE GENE EXPRESSION (1996)

It is believed that qualitative changes in thyroid peroxidase (TPO) cause decreased enzyme activity in differentiated thyroid carcinoma. To re-evaluate TPO expression in thyroid cancer, TPO mRNA expression was compared with TPO protein expression in 38 samples of thyroid tissue obtained from patients with various thyroid diseases. In Northern blot studies, while TPO mRNA was highly expressed in tissues from all 18 benign lesions, it was strongly suppressed in 14 tumours, including 12 out of 12 papillary carcinomas, one of seven follicular carcinomas, and one medullary carcinoma. TPO mRNA was not detected in six carcinomas, of which four were papillary, one follicular, and one medullary, by the usual Northern blot method. The 14 cases with strong underexpression of TPO mRNA were very weakly stained with anti-TPO monoclonal antibody 38E, whereas all 18 benign tissues were strongly stained. Moreover, a comparative study of TPO expression by Northern blot and immunohistochemical analysis revealed a positive correlation between TPO mRNA expression and the staining intensity of TPO protein. These results suggest that strong suppression of TPO mRNA transcription causes low TPO activity in papillary carcinoma; immunohistochemical loss of TPO may be a useful diagnostic marker. TPO mRNA expression in differentiated thyroid carcinomas did not always correlate with the mRNA expression of thyroglobulin, thyroid stimulating hormone receptor, and thyroid transcription factor 1.
Caspase-dependent Ceramide Production in Fas- and HLA Class I-mediated Peripheral T Cell Apoptosis (1998)

We recently demonstrated that the engagement of HLA class I alpha1 domain induced Fas-independent apoptosis in human T and B lymphocytes. We analyzed the signaling pathway involved in HLA class I-mediated apoptosis in comparison with Fas (APO-1, CD95)-dependent apoptosis. The mouse mAb90 or the rat YTH862 monoclonal antibodies which bind the human HLA class I alpha1 domain induced the production of ceramide which was blocked by addition of the phosphatidylcholine-dependent phospholipase C inhibitor, D609. Furthermore, HLA class I-mediated apoptosis involved at least two different caspases, an interleukin-1 converting enzyme-like protease and another protease inhibited by the CPP32-like protease inhibitor Ac-DEVD-CHO. Despite similarity between Fas and HLA class I signaling pathways, we failed to demonstrate any physical association between these two molecules. We also report that the pan-caspase inhibitory peptide zVAD-fmk, but not Ac-DEVD-CHO and Ac-YVAD-CHO, inhibited decrease of mitochondrial transmembrane potential and generation of ceramide induced by anti-HLA class I and anti-Fas monoclonal antibodies, whereas all three peptides efficiently inhibited apoptosis. Altogether these results suggest that signaling through Fas and HLA class I involve caspase(s), targeted by zVAD-fmk, which act upstream of ceramide generation and mitochondrial events, whereas interleukin-1 converting enzyme-like and CPP32-like proteases act downstream of the mitochondria.
Antacid provides better restoration of glandular structures within the gastric ulcer scar than omeprazole. (1994)

Mucosa of healed gastric ulcers displays histological abnormalities that are possibly the basis of ulcer recurrence. The influence of antacid and omeprazole treatment was studied on the quality of ulcer healing. Sixty four rats with gastric cryoulcers were treated daily either with placebo, antacid, omeprazole, or antacid plus omeprazole. Ulcer size was measured three times per week with a novel video endoscopic method. Prostaglandin generation (day 6), cell proliferation (day 8 and 15), height and cell composition of ulcer margin (day 8), and mucosal scar (day 15) were quantitatively assessed. Antacid, omeprazole, and antacid plus omeprazole significantly accelerated ulcer healing predominantly during days 3-8. Compared with placebo, the height of ulcer margin and mucosal ulcer scar was significantly increased in antacid (+7 and +9% respectively) and significantly decreased in omeprazole (-33 and -22% respectively) and antacid plus omeprazole (-26 and -18% respectively) treated rats. The number of bromodeoxyuridine labelled cells (+42%, day 8), epithelial cell mass (+42%, day 15), and the ratios of epithelial cells/connective tissue (+73%, day 15) and epithelial cells/gland lumen (+100%, day 15) were significantly increased in antacid treated rats. In conclusion, both antacid and omeprazole accelerate ulcer healing but antacid provides a better quality of healing. This advantage is lost by cotreatment with omeprazole.
Gas chromatographic analysis of amino acids as the N-heptafluorobutyryl isobutyl esters. (1987)

The N-heptafluorobutyryl isobutyl derivatives of proteic amino acids are well resolved by gas chromatography and form the basis of a convenient, rapid assay. The derivatives are prepared by acid-catalyzed esterification at 120 degrees C for 20 min in 3N HCl-isobutanol followed by acylation with heptafluorobutyric anhydride at 150 degrees C for 10 min. The reaction sequence is performed without any transfers or extractions and thus is compatible with microscale analysis. A complete proteic amino acid profile can be completed in less than 20 min by using a packed column or less than 10 min by using a capillary column in combination with an elevated oven temperature program rate. Physiological sample matrixes, which frequently contain a complex mixture of components, and thus require maximum resolution, can be assayed in less than 1 h using a program rate of 4 degrees C/min. A capillary column is recommended for this application. Capillary column chromatography, in combination with a nitrogen-specific detector, is useful for identifying and assaying nonproteic amino acids in physiological sample matrixes. Frequently, a prior cleanup of the sample can be avoided.
Retrofitting vectors for Escherichia coli-based artificial chromosomes (PACs and BACs) with markers for transfection studies. (1997)

P1-based artificial chromosomes (PACs) and bacterial artificial chromosomes (BACs) have significantly expanded the size of fragments from eukaryotic genomes that can be stably cloned in Escherichia coli as plasmid molecules. Functional characterization of a gene within a given PAC or BAC clone often requires transferring the DNA into eukaryotic cells for transient or long-term expression. To facilitate transfection studies, we have developed protocols using the Notl restriction sites of any PAC or BAC clone to introduce a transfection reporter gene, lacZ, together with a selectable marker, neo. This enables transfected cells to be detected by X-Gal staining to verify DNA uptake, and clones of stably transformed cells may be selected for in the presence of the antibiotic G418. The same retrofitting protocols may be applied with other markers of interest to extend the functionality of PAC and BAC libraries, and specialized aspects of such manipulation of E. coli-based artificial chromosomes are outlined.
Base Catalysed Pyrimidine Synthesis Using Microwave (2003)

An environmentally benign approach for the synthesis of 2-substituted-4,6-diaryl pyrimidines using inorganic solid supports for its catalytic role as well as an energy transfer medium is described. The methodology eliminates the usage of solvent during the reaction. The reaction time is brought down from hours to minutes along with yield enhancement. The rate enhancement and high yield is attributed to the coupling of solvent free conditions with microwaves. Further, the role of base is studied in the reaction and it is concluded that microwave assisted basic alumina catalysed reaction is the best in terms of catalysis as well as reaction time and yield.
Molecular characterization and copy number of SMN1, SMN2 and NAIP in Chinese patients with spinal muscular atrophy and unrelated healthy controls (2015)

The copy numbers and gene structures of SMA-related genes were different in Chinese SMA patients and healthy controls.
Modulation of potassium channels by protein tyrosine kinase inhibitors (1994)

Exposure of non-excitatory cells to the tyrosine kinase (PTK) inhibitors, genistein, herbimycin A, and tyrphostin, induced at least two families of K+ currents. The first, a TEA-insensitive slow-inactivating K+ current, is induced within 3 min following treatment with 140 mM genistein or 100 nM herbimycin A. The second current, a TEA-sensitive delayed rectifier, is induced within 30 min following treatment with 50 mM genistein or 10 nM herbimycin A. Currents with similar biophysical and pharmacological characteristics are induced in these cells following exposure to ionizing radiation. The radiation-induced currents are inhibited by pretreatment with the free radical scavenger, N-Acetyl L-Cysteine, or by pretreatment with the protein kinase C inhibitor, staurosporine; those induced by PTK inhibitors are not. The latter, therefore, do not appear to be mediated through free radicals or require serine/threonine phosphorylation for activation. Once the channels are activated by the PTK inhibitors, phosphorylation of the channel at serine/threonine residues results in slower inactivation of the induced current. We propose that protein tyrosine phosphorylation of the K+ channel protein itself or of a factor that interacts with it maintains the K+ channels of non-excitatory cells in a closed state. Following exposure to ionizing radiation, free radical-induced activation of serine/threonine kinase(s) results in phosphorylation of the channel and/or inactivation of a tyrosine kinase that in turn leads to activation of the K+ channels.
Combined Effect of Antiretroviral Therapy and Blockade of IDO in SIV-Infected Rhesus Macaques (2009)

Increased activity of IDO, which catalyzes the degradation of Trp into kynurenine (Kyn), is observed during HIV/SIV infection, and it may contribute to the persistence of HIV/SIV by suppressing antiviral T cell responses. We administered the IDO inhibitor 1-methyl-d-tryptophan (d-1mT) for 13 days to SIV-infected rhesus macaques receiving antiretroviral therapy (ART). d-1mT treatment increased the plasma levels of Trp, without reducing the levels of Kyn, suggesting only a partial effect on IDO enzymatic activity. Surprisingly, d-1mT significantly reduced the virus levels in plasma and lymph nodes of ART-treated animals with incomplete responsiveness to ART. In SIV-infected animals that were not receiving ART, d-1mT was ineffective in reducing the plasma viral load and had only a marginal effect on the plasma Kyn/Trp ratio. Increased IDO and TGF-beta mRNA expression in lymph nodes of ART-treated macaques after d-1mT treatment suggested that compensatory counterregulatory mechanisms were activated by d-1mT, which may account for the lack of effect on plasma Kyn. Finally, d-1mT did not interfere with the ART-induced T cell dynamics in lymph nodes (increased frequency of total CD4 T cells, increase of CD8 T cells expressing the antiapoptotic molecule Bcl2, and reduction of regulatory T cells). Thus, d-1mT appeared to synergize with ART in inhibiting viral replication and did not interfere with the beneficial immunologic effects of ART. Further studies are required to elucidate the immunologic or virologic mechanism by which d-1mT inhibited SIV replication in vivo.
General Classification of Dispersing Agents and Adsorption of Surfactants at the Solid/Liquid Interface (2012)

This chapter contains sections titled: Classification of Dispersing Agents References
Nutritional value of dried fermentation biomass, hydrolyzed porcine intestinal mucosa products, and fish meal fed to weanling pigs1 (2012)

Dried fermentation biomass (DFB) and hydrolyzed porcine intestinal mucosa are co-products of L-Lys • HCl production and heparin extraction, respectively. Three experiments were conducted to determine standardized ileal digestibility (SID) of AA (Exp. 1), concentration of DE and ME (Exp. 2), and standardized total tract digestibility (STTD) of P (Exp. 3) in DFB and 2 hydrolyzed porcine intestinal mucosa products (PEP50 and PEP2+), and compare these values with values for fish meal. In Exp. 1, 12 ileal cannulated barrows (BW = 11.5 ± 1.1 kg) were allotted to a replicated 6 × 6 Latin square design with 6 diets and 6 periods. A N-free diet, diet based on soybean meal (SBM), and 4 diets based on a combination of SBM and DFB, PEP50, PEP2+, or fish meal were formulated. With the exception of Lys, there were no differences in SID of indispensable AA between DFB and fish meal. Except for Thr, no differences in SID of indispensable AA between PEP50 and fish meal were observed, but SID of all indispensable AA, except Lys and Trp, was less (P < 0.05) in PEP2+ than in the other ingredients. In Exp. 2, 40 barrows (BW = 12.8 ± 1.4 kg) were allotted to 5 diets with 8 pigs/diet. A basal diet containing 96.4% corn and 4 diets containing corn and DFB, PEP50, PEP2+, or fish meal were formulated. The DE (5,445 kcal/kg DM) and ME (5,236 kcal/kg DM) in DFB were greater (P < 0.01) than in PEP50 (4,758 and 4,512 kcal/kg DM for DE and ME, respectively) and fish meal (4,227 and 3,960 kcal/kg DM for DE and ME, respectively). Also, DE in DFB was greater (P < 0.01) than in PEP2+ (4,935 kcal/kg DM), but ME in DFB was not different from that in PEP2+ (4,617 kcal/kg DM). Furthermore, DE in PEP50 and PEP2+ were greater (P < 0.01) than in fish meal, but ME did not differ from that in fish meal. In Exp. 3, 40 barrows (BW = 12.4 ± 1.3 kg) were randomly allotted to 5 diets with 8 pigs/diet. A P-free diet and 4 diets in which the sole source of P was from DFB, PEP50, PEP2+, or fish meal were formulated. The STTD of P in DFB (96.9%) and PEP2+ (97.6%) were greater (P < 0.01) than in PEP50 and fish meal (76.2% and 68.5%, respectively), and STTD of P in PEP50 was greater (P < 0.01) than in fish meal. In summary, SID of most indispensable AA did not differ among DFB, PEP50, and fish meal, but DE and ME and STTD of P in DFB were greater than in PEP50 and fish meal.
A Salmon Thrombin-Fibrin Bandage Controls Arterial Bleeding in a Swine Aortotomy Model (2005)

Fibrin dressing using salmon-derived thrombin and fibrinogen is effective in controlling severe, uncontrolled bleeding. This dressing may offer an alternative to dressings composed of human coagulation proteins.
Reversible thermal behavior of the layered double hydroxide of Mg with Al: mechanistic studies (2000)

The layered double hydroxide (LDH) of Mg with Al decomposes at 450 °C to yield a mixed metal oxide. The oxide reconstructs back to the parent LDH either on cooling in air or soaking in water. This reversible thermal behaviour was attributed to the formation of an unstable defect rocksalt phase (comprising Al3+ ions partially substituting for Mg2+ in MgO) on decomposition of the LDH. However a simple oxide mixture of MgO and Al2O3 taken in the 6∶1 molar ratio is also found to yield a LDH-like phase when soaked in an aqueous solution of a suitable anion, suggesting that the reconstruction occurs through a simple dissolution–reprecipitation mechanism. The formation of the defect rocksalt phase is not a necessary precondition for reconstruction. However, the kinetics of the reconstruction reaction depends upon the nature of the anion and the thermal history of the oxides. The presence of carbonate ions and unsintered oxides hastens the reconstruction reaction.