gebhart/patrepeval huggingface dataset:
A versatile and scalable strategy for glycoprofiling bifidobacterial consumption of human milk oligosaccharides (2008)

Human milk contains approximately 200 complex oligosaccharides believed to stimulate the growth and establishment of a protective microbiota in the infant gut. The lack of scalable analytical techniques has hindered the measurement of bacterial metabolism of these and other complex prebiotic oligosaccharides. An in vitro, multi-strain, assay capable of measuring kinetics of bacterial growth and detailed oligosaccharide consumption analysis by FTICR-MS was developed and tested simultaneously on 12 bifidobacterial strains. For quantitative consumption, deuterated and reduced human milk oligosaccharide (HMO) standards were used. A custom software suite developed in house called Glycolyzer was used to process the large amounts of oligosaccharide mass spectra automatically with (13)C corrections based on de-isotoping protocols. High growth on HMOs was characteristic of Bifidobacterium longum biovar infantis strains, which consumed nearly all available substrates, while other bifidobacterial strains tested, B. longum bv. longum, B. adolescentis, B. breve and B. bifidum, showed low or only moderate growth ability. Total oligosaccharide consumption ranged from a high of 87% for B. infantis JCM 7009 to only 12% for B. adolescentis ATCC 15703. A detailed analysis of consumption glycoprofiles indicated strain-specific capabilities towards differential metabolism of milk oligosaccharides. This method overcomes previous limitations in the quantitative, multi-strain analysis of bacterial metabolism of HMOs and represents a novel approach towards understanding bacterial consumption of complex prebiotic oligosaccharides.
On-column conductivity detector for capillary zone electrophoresis (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOn-column conductivity detector for capillary zone electrophoresisXiaohua. Huang, Teng Ke J. Pang, Manuel J. Gordon, and Richard N. ZareCite this: Anal. Chem. 1987, 59, 23, 2747–2749Publication Date (Print):December 1, 1987Publication History Published online1 May 2002Published inissue 1 December 1987https://pubs.acs.org/doi/10.1021/ac00150a004https://doi.org/10.1021/ac00150a004research-articleACS PublicationsRequest reuse permissionsArticle Views304Altmetric-Citations164LEARN 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
Chronic Oral Nicotine Normalizes Dopaminergic Function and Synaptic Plasticity in 1-Methyl-4-Phenyl-1,2,3,6-Tetrahydropyridine-Lesioned Primates (2006)

Our recent studies show that chronic oral nicotine partially protects against striatal damage in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-treated nonhuman primates. To identify the cellular changes associated with this protective action, we investigated the effects of nicotine treatment on stimulus-evoked dopamine release, dopamine turnover, and synaptic plasticity in striatum from lesioned and unlesioned animals. Monkeys were chronically (6 months) treated with nicotine in the drinking water and subsequently lesioned with the dopaminergic neurotoxin MPTP (6 months) while nicotine was continued. Nigrostriatal damage increased nicotinic acetylcholine receptor (nAChR)-mediated fractional dopamine release from residual terminals, primarily through changes in alpha3*/alpha6* nAChRs. In contrast, fractional receptor-evoked dopamine release was similar to control in unlesioned and lesioned animals with chronic oral nicotine. Long-term nicotine administration also attenuated the enhanced K(+)-evoked fractional dopamine release from synaptosomes of MPTP-lesioned animals, suggesting that nicotine treatment had a generalized effect on dopaminergic function. This premise was further supported by experiments showing that nicotine dosing decreased the elevated dopamine turnover that occurs after nigrostriatal damage. We next investigated changes in synaptic plasticity with lesioning and nicotine treatment. Nicotine treatment alone enhanced synaptic plasticity by lowering the threshold for long-term depression (LTD) in the corticostriatal pathway. MPTP lesioning led to a loss of LTD, a measure of short-term synaptic plasticity. In contrast, LTD was preserved in nicotine-treated lesioned animals. Thus, the present data show that the disruptions in striatal dopaminergic function after nigrostriatal damage were attenuated with chronic nicotine administration. These cellular alterations may underlie the ability of nicotine to maintain/restore normal function with nigrostriatal damage.
Transendothelial Migration of Colon Carcinoma Cells Requires Expression of E-selectin by Endothelial Cells and Activation of Stress-activated Protein Kinase-2 (SAPK2/p38) in the Tumor Cells (2001)

Adhesion and migration of tumor cells on and through the vascular endothelium are critical steps of the metastatic invasion. We investigated the roles of E-selectin and of stress-activated protein kinase-2 (SAPK2/p38) in modulating endothelial adhesion and transendothelial migration of HT-29 colon carcinoma cells. Tumor necrosis factor alpha (TNF alpha) strongly increased the expression of E-selectin in human umbilical vein endothelial cells (HUVEC). This effect was independent of the activation of SAPK2/p38 induced by TNF alpha. Adhesion of HT-29 cells on a monolayer of HUVEC pretreated with TNF alpha was dependent on E-selectin expression but was independent of SAPK2/p38 activity of both HUVEC and tumor cells. The adhesion of HT-29 cells to E-selectin-expressing HUVEC led to the activation of SAPK2/p38 in the tumor cells as reflected by the increased phosphorylation of the actin-polymerizing factor HSP27 by mitogen-activated protein kinase 2/3, a direct target of SAPK2/p38. Moreover, a recombinant E-selectin/Fc chimera quickly increased the activation of SAPK2/p38 in HT-29 cells. Blocking the increased activity of SAPK2/p38 of HT-29 cells by SB203580 or by expressing a dominant negative form of SAPK2/p38 inhibited their transendothelial migration. Similarly, HeLa cells stably expressing a kinase-inactive mutant of SAPK2/p38 showed a decreased capacity to cross a layer of HUVEC. Overall, our results suggest that the regulation of transendothelial migration of tumor cells involves two essential steps as follows: adhesion to the endothelium through adhesion molecules, such as E-selectin, and increased motogenic potential through adhesion-mediated activation of the SAPK2/p38 pathway.
Determination of the Area of Skin Capable of Being Covered by the Application of 250 mg of 5% Imiquimod Cream (2004)

BACKGROUND Five percent imiquimod cream is FDA-approved for the treatment of genital and perianal warts and actinic Keratosis. The manufacturer recommends that a single sachet containing 250 mg of 5% imiquimod cream (12.5 mg of imiquimod) is adequate for a single use and is sufficient to cover a wart area of up to 20 cm2. OBJECTIVE To determine the maximal area of skin that can be evenly covered by 250 mg of 5% imiquimod cream that is contained in one single-use sachet. METHODS The contents of one 250-mg single-use sachet of 5% imiquimod cream were mixed with less than 1 mg of fluorescein sodium. The cream was applied evenly onto the abdomen of two Yorkshire female pigs and onto the medial and lateral aspects of the upper left arm of a human subject. The area of application was then measured. RESULTS The average area obtained on the pig skin was 196 cm2. The area covered on the human subject was 386 cm2. CONCLUSION We have found that one sachet of 250 mg of 5% imiquimod cream can be applied to an area of skin up to 386 cm2. In light of the increasing use of 5% imiquimod cream in the treatment of cutaneous diseases, such as actinic keratoses, which affect larger areas of skin than genital warts, a more efficient use of 5% imiquimod cream may make this medication a more cost-effective treatment modality.
EVIDENCE CONCERNING LIQUID STRUCTURE (1961)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Serum glycoproteins in cancer patients: First report of correlations within vitro andin vivo parameters of cellular immunity (1980)

Serum levels of proteins previously shown to be elevated [acute-phase proteins (APP)-haptoglobin, alpha 1-acid glycoprotein, alpha 1-antitrypsin] or depressed (alpha 2 HS-glycoprotein, prealbumin, albumin) in cancer patients were correlated with tumor extent, in vitro lymphocyte reactivity (LR) to phytohemagglutinin (PHA), and quantitative delayed hypersensivity (DH) to dinitrochlorobenzene (DNCB) in 147 preoperative patients with operable solid malignancies either confined to the primary site or with regional spread only. Compared to 58 normal controls, levels of the APP were significantly elevated, alpha 2 HS-glycoprotein and prealbumin depressed, and albumin levels unchanged in patients with either local or regional tumors. In patients with normal DH to DNCB, the APP were higher and prealbumin was lower than in controls; in patients with impaired DH to DNCB, haptoglobin and alpha 1-acid glycoprotein were higher and alpha 2 HS-glycoprotein and prealbumin lower than in patients with normal DH to DNCB. Albumin levels did not differ from normals in any of the groups. Serum protein levels appeared to be more related to the immune status of the patient than to tumor extent. The levels of the three APP correlated directly with each other but inversely with alpha 2 HS-glycoprotein and prealbumin; levels of alpha 2 HS-glycoprotein and prealbumin correlated directly with each other. Levels of haptoglobin and alpha 1-acid glycoprotein correlated inversely with LR to PHA; however, levels of alpha 2 HS-glycoprotein correlated directly with LR to PHA, and uniquely the levels of alpha 2 HS-glycoprotein and LR to PHA both showed similar changes for each of the four quantitative levels of DH to DNCB measured in the cancer patients. The data show that the proteins studied, except for albumin, correlate inversely (APP) or directly (alpha 2 HS-glycoprotein and prealbumin) with in vitro and in vivo parameters of cellular immunity. The results provide a rationale for attempts to improve depressed cellular immunity by lowering circulating levels of APP, as is being attempted in ongoing trials using plasmapheresis, and assessing the effect of exogenous alpha 2 HS-glycoprotein or prealbumin in patients with low levels of these glycoproteins and depressed cellular immunity. The correlations between serum glycoprotein levels and in vitro and in vivo parameters of cellular immunity lend rationale to investigations of the interactions of serum glycoproteins and blood cells having immunologic function that determine the level of cellular immunity expressed in vivo.
Human gamma-trace, a basic microprotein: amino acid sequence and presence in the adenohypophysis. (1982)

The amino acid sequence of human gamma-trace, a basic microprotein without known function, was determined by automated Edman degradations of the carboxymethylated polypeptide chain and of fragments obtained by cyanogen bromide treatment and tryptic digestion after blocking of lysine residues. The single polypeptide chain contained 120 residues, and the calculated Mr was 13,260. A proline residue at position 3 was partly hydroxylated. The presence of gamma-trace in a significant proportion of the cells in the anterior lobe of simian and human pituitary glands was demonstrated by immunohistochemical procedures with a rabbit antiserum against human gamma-trace. The tissue localization and amino acid sequence of gamma-trace indicated that this protein is connected with the peptidergic gastroenteropancreatic neuroendocrine system.
ACG, the initiator codon for a Sendai virus protein. (1988)

Deletion and site-directed point mutants of the polycistronic P/C mRNA of Sendai virus revealed that one of the nonstructural proteins of this virus, the C' protein, initiates from an ACG codon. This ACG codon occurs in an optimum sequence context and precedes the first AUG of the P/C mRNA. The results presented in this communication are consistent with the concept that the ribosomes scan the P/C mRNA to initiate several proteins from its different initiator codons. The arrangement of several weak initiator codons in tandem in an mRNA, i.e. non-AUG in optimum sequence context and AUG in suboptimum sequence context, may represent an alternate means to regulate gene expression in eukaryotes and their viruses.
You Might Be Interested (2001)

In deploring the “mess that is medical information” in a column entitled, “Doctors’ Information: excessive, crummy and bent,” the editor of one of the most prestigious medical journals (Br Med J 315:9) notes that “most of what doctors do is of small benefit and potentially harmful.”
Ablation of the Proapoptotic Genes Chop or Ask1 Does Not Prevent or Delay Loss of Visual Function in a P23H Transgenic Mouse Model of Retinitis Pigmentosa (2014)

The P23H mutation in rhodopsin (Rho(P23H)) is a prevalent cause of autosomal dominant retinitis pigmentosa. We examined the role of the ER stress proteins, Chop and Ask1, in regulating the death of rod photoreceptors in a mouse line harboring the Rho(P23H) rhodopsin transgene (GHL(+)). We used knockout mice models to determine whether Chop and Ask1 regulate rod survival or retinal degeneration. Electrophysiological recordings showed similar retinal responses and sensitivities for GHL(+), GHL(+)/Chop(-/-) and GHL(+)/Ask1(-/-) animals between 4-28 weeks, by which time all three mouse lines exhibited severe loss of retinal function. Histologically, ablation of Chop and Ask1 did not rescue photoreceptor loss in young animals. However, in older mice, a regional protective effect was observed in the central retina of GHL(+)/Chop(-/-) and GHL(+)/Ask1(-/-), a region that was severely degenerated in GHL(+) mice. Our results show that in the presence of the Rho(P23H) transgene, the rate of decline in retinal sensitivity is similar in Chop or Ask1 ablated and wild-type retinas, suggesting that these proteins do not play a major role during the acute phase of photoreceptor loss in GHL(+) mice. Instead they may be involved in regulating secondary pathological responses such as inflammation that are upregulated during later stages of disease progression.
Pharmacological study of the antitussive and respiratory-analeptic properties of N-(2'-ethylpyrrolidino)diphenylacetamide hydrochloride (F 1459). (1983)

The antitussive and respiratory stimulant properties of N-(2'-ethylpyrrolidino)diphenylacetamide hydrochloride (F 1459) in animals are reported. In the mechanical stimulation of the trachea in guinea pigs and after intraperitoneal administration of the product, F 1459 showed a better antitussive action as compared to oxeladin, zipeprol, codeine and clobutinol. Low intraduodenal doses of F 1459 also reduced in cats the cough induced by the electrical stimulation of the superior laryngeal nerve. In anesthetized dogs whose respiratory functions had been depressed by morphine, F 1459 significantly increased the volume inspired per minute, an effect not due to any uncoupling effect on oxidative phosphorylation. F 1459 has local anesthetic and broncholytic properties that may play a role in the mechanism of its antitussive action. Contrarily to codeine, the test compound did not induce a decrease in the intestinal transit.
Micellization and Gelation of Aqueous Solutions of a Triblock Copolymer Studied by Rheological Techniques and Scanning Calorimetry (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMicellization and Gelation of Aqueous Solutions of a Triblock Copolymer Studied by Rheological Techniques and Scanning CalorimetrySoren Hvidt, Erling B. Joergensen, Wyn Brown, and Karin SchillenCite this: J. Phys. Chem. 1994, 98, 47, 12320–12328Publication Date (Print):November 1, 1994Publication History Published online1 May 2002Published inissue 1 November 1994https://pubs.acs.org/doi/10.1021/j100098a030https://doi.org/10.1021/j100098a030research-articleACS PublicationsRequest reuse permissionsArticle Views626Altmetric-Citations197LEARN 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 options Get e-Alerts
A Smart Monte Carlo Technique for Free Energy Simulations of Multiconformational Molecules. Direct Calculations of the Conformational Populations of Organic Molecules (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA Smart Monte Carlo Technique for Free Energy Simulations of Multiconformational Molecules. Direct Calculations of the Conformational Populations of Organic MoleculesHanoch Senderowitz, Frank Guarnieri, and W. Clark StillCite this: J. Am. Chem. Soc. 1995, 117, 31, 8211–8219Publication Date (Print):August 1, 1995Publication History Published online1 May 2002Published inissue 1 August 1995https://pubs.acs.org/doi/10.1021/ja00136a020https://doi.org/10.1021/ja00136a020research-articleACS PublicationsRequest reuse permissionsArticle Views395Altmetric-Citations89LEARN 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
Susceptibility of Anaerobic Bacteria <i>in vitro </i>to 23 Antimicrobial Agents (1980)

589 isolates of anaerobic bacteria, including 127 isolates of Bacterioides fracilis, were tested against 23 antimicrobial agents. At their usually achievable serum levels, carbenicillin, ticarcillin, mezlocillin and piperacillin; cefoxitin, minocycline, doxycycline, clindamycin, chloramphenicol and rifampin were effective against more than 80% of B. fragilis isolates. At usual therapeutic doses, penicillin (PEN), ampicillin (AMP), cyclacillin (CYC), cephalothin (CT), cefazolin (CZ), cephradine (CPD), cefamandole (CMD), cefaclor (CCL), cefuroxime (CRX), spectinomycin (SPT), tetracycline (TET), ethambutol (EMB) and isoniazid (INH) were ineffective against B. Fragilis. However, high and clinically tolerated doses of PEN, CMD and SPT inhibited more than 80% of B. fragilis isolates, but AMP, CYC, CT, CZ, CPD, CCL and CRX, TET, EMB and INH remained totally ineffective against B. fragilis. The therapeutic merits of these antibiotics are discussed.
Pruritus of Cholestasis (2014)

Cholestasis is defined as impaired secretion of bile.1 Pruritus is a complication of cholestasis including that associated with mutations in genes that code for transporters in the hepatocyte2,3 and from inflammatory liver diseases.4,5 In this regard, pruritus is more common in conditions characterized by bile duct inflammatory destruction and ductopenia including primary bile cirrhosis primary biliary cirrhosis (PBC)5 than in those characterized by hepatocellular injury such as chronic viral hepatitis.4 The pruritus of cholestasis tends to be generalized. It leads to scratching, sometimes violent, resulting in excoriations and prurigo nodularis. This type of pruritus can lead to sleep deprivation, and in some patients, to suicidal ideations. Intractable pruritus from liver disease is an indication for liver transplantation even in the absence of liver failure.6,7 Accordingly, pruritus is a complication of liver disease that requires specific management and intense research in an effort to design effective antipruritic medications.
Processing of exogenous liposome-encapsulated antigens in vivo generates class I MHC-restricted T cell responses (1992)

Acid-sensitive liposomes have been developed for cytosolic delivery of encapsulated substances. We now demonstrate delivery of liposome-encapsulated Ag into the class I MHC Ag processing pathway in peritoneal macrophages in vitro using several types of acid-sensitive liposomes, including those composed of dioleoylphosphatidylethanolamine (DOPE)/palmitoylhomocysteine, DOPE/cholesterol hemisuccinate, DOPE/dioleoylsuccinylglycerol, and DOPE/dipalmitoylsuccinylglycerol. Our previous studies showed that acid-resistant liposomes (dioleoylphosphatidylcholine/dioleoylphosphatidylserine) did not engender class I-mediated presentation in vitro. However, in vivo immunization with OVA encapsulated in acid-resistant as well as acid-sensitive liposomes generated class I MHC-restricted T cell responses, as determined by subsequent in vitro cytotoxicity assays using OVA-transfected target cells. Target lysis by these cells was OVA- and class I MHC (Kb)-specific. This response was not generated by immunization with equivalent amounts of soluble OVA. Thus, a pathway for in vivo class I processing of Ag encapsulated in acid-resistant liposomes has been missed in vitro, perhaps because it is dependent on specific populations of APC or interactions between cells that have not been reconstituted in vitro. This pathway may explain the ability of many exogenous particulate Ag (liposomes, bacteria, parasites, and mammalian cells) to generate class I MHC-restricted T cell responses.
Chemical and Pharmacological Studies on N-Resulfated Heparin (1962)

SummaryA method for synthesis of radioactive heparin of high unit activity and radioactivity has been described using a process of N-desulfation and N-resulfation. Comparison of the biological identity of the radioactive material with commercial heparin has been made. N-resulfated S35 heparin appears to be similar to biosynthetic S35 heparin in both its clearing and anticoagulant activity as well as its ultimate fate and distribution in the body.