gebhart/patrepeval huggingface dataset:
H19 RNA Binds Four Molecules of Insulin-like Growth Factor II mRNA-binding Protein (2000)

H19 RNA is a major oncofetal 2.5-kilobase untranslated RNA of unknown function. The maternally expressed H19 gene is located 90 kilobase pairs downstream from the paternally expressed insulin-like growth factor II (IGF-II) gene on human chromosome 11 and mouse chromosome 7; and due to their reciprocal imprinting and identical spatiotemporal expression, it is assumed that the two genes are functionally coupled. Here we show that human H19 RNA contains four attachment sites for the oncofetal IGF-II mRNA-binding protein (IMP) with apparent K(d) values in the 0.4-1.3 nm range. The multiple attachment sites are clustered within a 700-nucleotide segment encoded by exons 4 and 5. This 3'-terminal segment targets H19 RNA to lamellipodia and perinuclear regions in dispersed fibroblasts where IMP is also localized. The results suggest that IMP participates in H19 RNA localization and provides a link between the IGF-II and H19 genes at post-transcriptional events during mammalian development.
Nucleotide sequence of the hag gene encoding flagellin of Escherichia coli (1986)

We determined the DNA sequence of the hag gene of Escherichia coli K-12 and deduced the primary structure of the flagellin consisting of 497 amino acid residues. Comparison of the amino acid sequence with those of other bacterial flagellins revealed a high homology in the NH2- and COOH-terminal regions.
Antagonism against Vibrio cholerae by diffusible substances produced by bacterial components of the human faecal microbiota (2001)

Cholera vibrios sometimes survive, probably in low-level silent populations, in the small intestine of chronic carriers or pass through the gastrointestinal tract of a few individuals without causing diarrhoea or colonisation. To understand these situations, the present study used plate cultures (ex-vivo test) to investigate the frequency of appearance of an inhibitory halo against Vibrio cholerae produced by faecal specimens from 92 healthy volunteers (40 females, 52 males) aged 4-61 years. The frequency of inhibitory halo was 20.6% in the whole group. An apparently higher percentage (27.3%) was observed in the age range 20-40 years when compared with the range 4-19 years (10.7%), but not the range 41-61 years (20.0%). Frequency was significantly higher in males (30.8%) than females (7.5%). The dominant microbiota of a volunteer whose faeces produced an inhibitory halo was isolated by plate culture of decimal dilutions in an anaerobic chamber. Potential isolates of 26 apparently different morphologies were associated with germ-free NIH mice. One week later, the inhibitory test showed an antagonistic halo around the faeces from the associated animals, but not from the axenic mice. Of the 26 bacteria isolated, two (Lactobacillus sp. and Peptostreptococcus sp.) produced a compound antagonistic against V. cholerae in an in-vitro assay. When bi-associated with germ-free mice those strains eliminated the vibrio from the intestinal ecosystem in c. 5 days.
Velocity-independent microfluidic flow cytometry (2002)

Pressure-driven flow in microfluidic channels is characterized by a distribution of velocities. This distribution makes it difficult to implement conventional flow cytometry data analysis. We have demonstrated a method to measure velocity as an independent parameter when performing microfluidic flow cytometry. This method allows velocity-independent analysis of particles such as beads or cells, and allows flow cytometry analysis of extended objects, such as long DNA molecules. It allows accurate flow cytometry in transient and nonuniform flows. This general measurement method could be used in the future to measure the velocity of particles in a variety of existing microfluidic devices without the need for changes in their design.
Mean shift, mode seeking, and clustering (1995)

Mean shift, a simple interactive procedure that shifts each data point to the average of data points in its neighborhood is generalized and analyzed in the paper. This generalization makes some k-means like clustering algorithms its special cases. It is shown that mean shift is a mode-seeking process on the surface constructed with a "shadow" kernal. For Gaussian kernels, mean shift is a gradient mapping. Convergence is studied for mean shift iterations. Cluster analysis if treated as a deterministic problem of finding a fixed point of mean shift that characterizes the data. Applications in clustering and Hough transform are demonstrated. Mean shift is also considered as an evolutionary strategy that performs multistart global optimization.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Mass loading, sleep apnea, and the pathogenesis of obesity hypoventilation. (1982)

To define the roles of mechanical loading, respiratory neuromuscular control, and sleep apnea in the pathogenesis of obesity hypoventilation, respiratory muscle drive and output, assessed by diaphragmatic electromyogram (EMGdi) and mouth occlusion pressure (P 0.15), respectively, were determined during CO2 chemostimulation in nonobese volunteers who were subjected to abdominal mass loading, and in three groups of markedly obese patients: eucapnic obese without sleep apnea (O), eucapnic obese with sleep apnea (OSA), and hypercapnic obese with sleep apnea (OH). The P0.15 responses were decreased in OSA and OH, but the EMGdi responses were not significantly different from those in control subjects. In O patients EMGdi responses were significantly greater than those in control subjects as well as those in OSA and OH patients. EMGdi and P0.15 responses increased in all nonobese subjects when they were subjected to mass loading. We conclude that both OSA and OH patients were equally unable to develop the expected increase in respiratory muscle drive and output. The presence of sleep apnea, possibly by causing nocturnal hypoxemia and/or sleep fragmentation, may result in impaired mass load compensation and predispose obese patients to develop hypercapnia.
CIRCULATING CONCENTRATIONS AND PRODUCTION OF CYTOKINES AND SOLUBLE RECEPTORS IN RHEUMATOID ARTHRITIS PATIENTS: EFFECTS OF A SINGLE DOSE METHOTREXATE (1994)

Methotrexate (MTX) is an effective treatment for RA and its effects may be partly due to cytokine modulation. Herein, we assessed the effects of a single MTX dose on the production and circulating concentrations of several cytokines and soluble receptors in 42 RA patients on three consecutive days. Three patient groups were studied: (a) 16 patients taking the first MTX dose, (b) 11 patients on chronic MTX treatment and (c) a control group of 15 patients not treated with MTX. Cytokine production was studied in peripheral blood mononuclear cells (PBMNC) and in a whole-blood culture system (WBCS). Group (a) had a more active disease according to laboratory parameters as well as higher circulating IL-6 levels (P = 0.002). The secretion of IL-1 beta by stimulated PBMNC (P = 0.008) was higher in this group and decreased significantly (P = 0.03) after a single MTX dose. No significant change in any parameter was observed after MTX in group (b). In the total patient group, circulating concentrations of IL-1 beta and TNF-alpha were low but blood cells showed a high capacity of production for these cytokines. In contrast for sTNFRs, high circulating levels but a limited in vitro production were observed. In conclusion, a single MTX dose may result in decreased production of IL-1 beta by PBMNC in patients with active RA. Furthermore, we observed an imbalance in the production of TNF-alpha and sTNFRs by peripheral blood cells of RA patients and propose that the WBCS is convenient for studying cytokine production in RA.
Chalcomycin Biosynthesis Gene Cluster from Streptomyces bikiniensis : Novel Features of an Unusual Ketolide Produced through Expression of the chm Polyketide Synthase in Streptomyces fradiae (2004)

Chalcomycin, a 16-membered macrolide antibiotic made by the bacterium Streptomyces bikiniensis, contains a 2,3-trans double bond and the neutral sugar D-chalcose in place of the amino sugar mycaminose found in most other 16-membered macrolides. Degenerate polyketide synthase (PKS)-specific primers were used to amplify DNA fragments from S. bikiniensis with very high identity to a unique ketosynthase domain of the tylosin PKS. The resulting amplimers were used to identify two overlapping cosmids encompassing the chm PKS. Sequencing revealed a contiguous segment of >60 kb carrying 25 putative genes for biosynthesis of the polyketide backbone, the two deoxysugars, and enzymes involved in modification of precursors of chalcomycin or resistance to it. The chm PKS lacks the ketoreductase and dehydratase domains in the seventh module expected to produce the 2,3-double bond in chalcomycin. Expression of PKS in the heterologous host Streptomyces fradiae, from which the tyl genes encoding the PKS had been removed, resulted in production of at least one novel compound, characterized as a 3-keto 16-membered macrolactone in equilibrium with its 3-trans enol tautomer and containing the sugar mycaminose at the C-5 position, in agreement with the structure predicted on the basis of the domain organization of the chm PKS. The production of a 3-keto macrolide from the chm PKS indicates that a discrete set of enzymes is responsible for the introduction of the 2,3-trans double bond in chalcomycin. From comparisons of the open reading frames to sequences in databases, a pathway for the synthesis of nucleoside diphosphate-D-chalcose was proposed.
Functional Independence Measure (WeeFIM) for Chinese Children: Hong Kong Cohort (2002)

We have created a normative functional independence profile for Chinese children by adapting the American-based WeeFIM. There were cultural differences when compared with American children. Interestingly, Chinese children in Hong Kong scored better than their American counterparts in domain 1 (self-care) in all ages. This might be attributable to early attendance in preschool settings where children are taught to tend to their needs. Even for domain 2 (mobility), the higher scores in younger Chinese children in Hong King (<3 years) might be explained by earlier attendance in preschool settings. The American children did catch up after 3 years. As for domain 3 (cognition), the local educational system emphasized reading, writing, memorizing materials, and social interaction. Thus, Chinese children in Hong Kong had better cognition scores until 42 months, when their American counterparts caught up by attending preschool. There are definitely environmental and cultural practices affecting functional independence in both ethnic groups, especially in the upper age range (>4 years) both in America and Hong Kong. Thus, a locally validated WeeFIM instrument should be adopted for Chinese children. Our study demonstrated that WeeFIM could be used as a functional independence measure for Chinese children. Hong Kong has a different cultural background compared with America; thus, usage of WeeFIM with different age criteria for achieving independence should be adopted.
Polymer Nanofibers via Nozzle-Free Centrifugal Spinning (2008)

We report on the unexpected finding of nanoscale fibers with a diameter down to 25 nm that emerge from a polymer solution during a standard spin-coating process. The fiber formation relies upon the Raleigh-Taylor instability of the spin-coated liquid film that arises due to a competition of the centrifugal force and the Laplace force induced by the surface curvature. This procedure offers an attractive alternative to electrospinning for the efficient, simple, and nozzle-free fabrication of nanoscale fibers from a variety of polymer solutions.
Metal ion catalysis during the exon-ligation step of nuclear pre-mRNA splicing: Extending the parallels between the spliceosome and group II introns (2000)

Mechanistic analyses of nuclear pre-mRNA splicing by the spliceosome and group II intron self-splicing provide insight into both the catalytic strategies of splicing and the evolutionary relationships between the different splicing systems. We previously showed that 3'-sulfur substitution at the 3' splice site of a nuclear pre-mRNA has no effect on splicing. We now report that 3'-sulfur substitution at the 3' splice site of a nuclear pre-mRNA causes a switch in metal specificity when the second step of splicing is monitored using a bimolecular exon-ligation assay. This suggests that the spliceosome uses a catalytic metal ion to stabilize the 3'-oxyanion leaving group during the second step of splicing, as shown previously for the first step. The lack of a metal-specificity switch under cis splicing conditions indicates that a rate-limiting conformational change between the two steps of splicing may mask the subsequent chemical step and the metal-specificity switch. As the group II intron, a true ribozyme, uses identical catalytic strategies for splicing, our results strengthen the argument that the spliceosome is an RNA catalyst that shares a common molecular ancestor with group II introns.
Neuromodulation for the treatment of urinary incontinence. (2008)

The prevalence of overactive bladder (OAB) in the United States ranges from 10% - 30%. The mainstay of treatment is anticholinergic medication. All agents have significant side effects and at least 30% of patients fail to respond. This paper reviews neuromodulation which involves the use of electrical stimulation of either the sacral or peripheral nerves to modify the behavior of the bladder. It is an option for patients who either cannot tolerate medications or fail therapy.
Treating Functional Impairment of Autism with Selective Serotonin-Reuptake Inhibitors (2004)

Benefits with SSRIs in treating functional impairments in autism have been observed. Response to therapy and adverse effects are individualized. Current evidence does not support selection of one SSRI over another for any impairment associated with autism.
Prognostic stratification of Dukes B colon cancer by a neoglycoprotein (2004)

Disease progression of tumors is accompanied by structural changes of the glycan chains of cellular glycoconjugates. Within the concept of the sugar code the presence of complementary receptors such as lectins translates changes in ligand presentation into biological effects, for example in growth regulation and adhesion. By introducing neoglycoproteins to histopathological colon cancer analysis the questions are addressed as to whether specific binding sites for main N- and O-glycan components are present and whether they harbor potential for prognostic predictions. Synthetic conjugation of fucose, lactose, and mannose derivatives to a carrier protein yielded neoglycoproteins for glycohistochemical analysis. The tumor panel included routinely fixed tissue sections from 67 cancer cases (15 Dukes A, 20 Dukes B, 15 Dukes C, and 17 metastatic tumors) and 6 hepatic metastases as well as 20 normal biopsy specimens as control. Quantitative image analysis determined the labeling index and the mean optical density in each case, separating tumor and peritumoral connective tissue. Specific carbohydrate-dependent binding with inter-individual heterogeneity was observed. The distinct staining profiles were not associated with disease stage or metastasis formation. Strong expression of lactose-binding sites in the peritumoral connective tissue especially in terms of the labeling index was significantly correlated with reduced survival in Dukes B patients (p=0.02). A similar tendency was observed in the Dukes C group. In conclusion, the application of the synthetic markers aimed at lectin detection defines lactose binding as new prognostic marker. It has potential relevance for improving the benefit from adjuvant therapy in Dukes B colorectal cancer patients. Technically, chemical ligand immobilization to an inert carrier can find useful application beyond glycosciences in the quest to extend the panel of tumor markers.
Barley seed coating with free and immobilized alkaline phosphatase to improve P uptake and plant growth (2012)

SUMMARY Coating barley seeds with free and immobilized alkaline phosphatase was investigated as a potential means to enhance plant utilization of accumulated soil phosphorus (P). Two coating techniques were studied: film-coating and pelleting. The highest phosphatase activity retention in the coating layer, ranging from 0·48 to 0·67, was observed when seeds were film-coated with phosphatase–polyresorcinol complex (PPC). The germination of seeds film-coated or pelleted with alkaline phosphatase ranged from 0·84 to 0·97 or 0·14 to 0·25, respectively. Low germination of the pelleted seeds was attributed to freezing the seeds in liquid nitrogen (N) for the layer coating formation. Pelleted seeds were not used in the remainder of the studies. Under pot culture conditions, an increase in the soil inorganic P was detected when the seeds were film-coated with phosphatase. Moreover, the film-coating significantly increased the P uptake by plants (between 25 and 31% after 35 days after planting (DAP)). The present study showed that the seed film-coating with free and immobilized phosphatase increased the phosphatase activity in the rhizosphere and the P uptake by plants.
Bioaccumulation From Mineral Oil-Wet and Synthetic Liquid-Wet Cuttings in an Estuarine Fish, Fundulus grandis (1991)

ABSTRACT The long-term effects of discharged oily drill cuttings on native fish populations are of major concern. This study investigates the uptake of oil and synthetic liquid by the mud minnow, Fundulus grandis. when exposed to three different concentrations of low-aromatic mineral oil-wet and synthetic liquid-wet cuttings in flow-through bioassay chambers. Fish were introduced into the flow-through bioassay system and cultured for 30 days. Water, cuttings, and fish were sampled routinely for analysis. Fish samples were dissected; gut and tissue samples were analyzed separately. Flow-through water was analyzed by extracting the water sampling tube absorbent. The cutting samples were analyzed by Soxhlet extraction. Fish tissue and gut samples were digested in sodium hydroxide and extracted with ether. The extracted organics in all the samples were analyzed by gas chromatograph!mass spectrometry. Gas chromatograph!mass spectrometry identified uptake of the mineral oil in fish tissue and gut samples for all cuttings treated with mineral oil-based mud (MOBM). No uptake was measured in any of the tissue samples for all cuttings treated with synthetic liquid-based mud (SBM). An accumulation of synthetic liquid was only detected in one sample of fish gut from the lowest concentration of SBM. The contrast in uptake between the mineral oil and the synthetic liquid is perhaps due to the greater molecular size of the synthetic liquid over that of the mineral oil. It is hypothesized that the greater molecular size of the synthetic liquid restricts uptake by gill and digestive structures. During the study, there was little migration of either base fluid from the cuttings. Hydrocarbon amounts in the water samples generally decreased during the 30-day test period. All collected organics were liberated as negligibly soluble microdroplets. Tests indicated no selective solubility of released microdroplets and little if any biodegradation for both SBM and MOBM.
Identification and partial characterization of multiple major allergens in peanut proteins (1998)

From the present study, we conclude that peanuts contain multiple allergens, of which six can be described as major allergens, Ara h2 included. In our population Ara h1 is not a major allergen. The recognition of peanut proteins by immunoglobulins is more diverse in PA individuals compared with NA individuals which, however, is not substantiated in the concentrations of peanut-specific immunoglobulins in plasma, other than IgE.
2-(Chloromethyl)-3,5-dioxahex-1-ene. An effective acetonylating reagent (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT2-(Chloromethyl)-3,5-dioxahex-1-ene. An effective acetonylating reagentXue Ping Gu, Nobuyuki Nishida, Isao Ikeda, and Mitsuo OkaharaCite this: J. Org. Chem. 1987, 52, 15, 3192–3196Publication Date (Print):July 1, 1987Publication History Published online1 May 2002Published inissue 1 July 1987https://pubs.acs.org/doi/10.1021/jo00391a003https://doi.org/10.1021/jo00391a003research-articleACS PublicationsRequest reuse permissionsArticle Views799Altmetric-Citations29LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Magnolia polyphenols attenuate oxidative and inflammatory responses in neurons and microglial cells (2013)

This study highlights the important role of NADPH oxidase in mediating oxidative stress in neurons and microglial cells and has unveiled the role of IFNγ in stimulating the MAPK/ERK1/2 signaling pathway for activation of NADPH oxidase in microglial cells. Hon and Mag offer anti-oxidative or anti-inflammatory effects, at least in part, through suppressing IFNγ-induced p-ERK1/2 and its downstream pathway.
Quinazoline antifolate thymidylate synthase inhibitors: heterocyclic benzoyl ring modifications (1991)

The synthesis is described of a series of C2-methyl-N10-alkylquinazoline-based antifolates in which the p-aminobenzoate ring is replaced by the heterocycles thiophene, thiazole, thiadiazole, pyridine, and pyrimidine. These were generally elaborated by the reaction of (bromomethyl)quinazoline 18 or its N3-[(pivaloyloxy)methyl]-protected derivative 36 with suitable heterocyclic amines although each heterocyclic system required its own particular synthetic approach. The compounds were tested as inhibitors of partially purified L1210 thymidylate synthase (TS). They were also examined for their inhibition of the growth of L1210 cells in culture. The thiophene system 7 and its related thiazole 8 gave analogues that were considerably more potent than the parent benzene series 2 as inhibitors of L1210 cell growth although in general these heterocycles were somewhat poorer inhibitors of the isolated TS enzyme. The enhanced cytotoxicities of the thiophene and thiazole analogues result, at least in part, from their efficient transport into the cells via the reduced folate carrier mechanism and very good substrate activity for folylpolyglutamate synthetase. The replacement of the C2-methyl group by C2-(fluoromethyl) and C2-(hydroxymethyl) substituents in the thiophene and thiazole series gave derivatives that were only slightly less potent inhibitors of the TS enzyme but which were considerably less cytotoxic.