gebhart/patrepeval huggingface dataset:
Effects of Histidine Supplementation on Global Serum and Urine 1H NMR-based Metabolomics and Serum Amino Acid Profiles in Obese Women from a Randomized Controlled Study (2017)

The aim of current study was to investigate the metabolic changes associated with histidine supplementation in serum and urine metabolic signatures and serum amino acid (AA) profiles. Serum and urine <sup>1</sup>H NMR-based metabolomics and serum AA profiles were employed in 32 and 37 obese women with metabolic syndrome (MetS) intervened with placebo or histidine for 12 weeks. Multivariable statistical analysis were conducted to define characteristic metabolites. In serum <sup>1</sup>H NMR metabolic profiles, increases in histidine, glutamine, aspartate, glycine, choline, and trimethylamine-N-oxide (TMAO) were observed; meanwhile, decreases in cholesterol, triglycerides, fatty acids and unsaturated lipids, acetone, and α/β-glucose were exhibited after histidine supplement. In urine <sup>1</sup>H NMR metabolic profiles, citrate, creatinine/creatine, methylguanidine, and betaine + TMAO were higher, while hippurate was lower in histidine supplement group. In serum AA profiles, 10 AAs changed after histidine supplementation, including increased histidine, glycine, alanine, lysine, asparagine, and tyrosine and decreased leucine, isoleucine, ornithine, and citrulline. The study showed a systemic metabolic response in serum and urine metabolomics and AA profiles to histidine supplementation, showing significantly changed metabolism in AAs, lipid, and glucose in obese women with MetS.
Functional Recovery of Rat Hind-Limb Allografts (2005)

Few papers have assessed the long-term functional recovery of animal limb allografts. In this study, the functional recovery of rat limb allografts was serially and quantitatively investigated for a period of 1 year. The donor's hind limb was orthotopically transplanted into the recipient. Fifteen recipients with allografts were treated with FK506. Functional recovery of the grafted limb was assessed serially by cutaneous reaction test, walking track analysis, and electrophysiologic evaluation. Sensibility improved to a similar extent in both isografts and allografts, and the recovery rate at 1 year was 68 percent, compared to the normal side. Sciatic function index significantly improved to - 70 points after 1 year. The amplitude recorded from the gastrocnemius muscle significantly improved, and the ratio compared to the normal side was 43 percent. Limb isografts and allografts treated with FK506 showed no significant differences in functional recovery. The data can be used as a reference standard for future investigations.
Arg362 and Tyr365 of the Botulinum Neurotoxin Type A Light Chain Are Involved in Transition State Stabilization (2002)

The botulinum neurotoxin type A (BoNT/A) light chain (LC) acts as zinc endopeptidase. The X-ray structure of the toxin demonstrated that Zn(2+) is coordinated by His(222) and His(226) of the Zn(2+) binding motif HisGluXXHis and Glu(261), whereas Glu(223) coordinates the water molecule required for hydrolysis as the fourth ligand. Recent analysis of a cocrystal of the BoNT/B LC and its substrate synaptobrevin 2 suggested that Arg(362) and Tyr(365) of the homologous BoNT/A may be directly involved in catalysis. Their role and that of Glu(350) which is also found in the vicinity to the active site were analyzed by site-directed mutagenesis. Various replacements of Arg(362) and substitution of Tyr(365) with Phe resulted in 79- and 34-fold lower k(cat)/K(m) values, respectively. These changes were provoked by decreased catalytic rates (k(cat)) and not by alterations of ground state substrate binding as evidenced by largely unchanged K(d) and K(m) values. None of these mutations affected the overall secondary structure or zinc content of the LC. These findings suggest that the guanidino group of Arg(362) and the hydroxyl group of Tyr(365) together accomplish transition state stabilization as was proposed for thermolysin, being the prototypical member of the gluzincin superfamily of metalloproteases. Mutation of Glu(350) dramatically diminished the hydrolytic activity which must partly be attributed to an altered active site fine structure as demonstrated by an increased sensitivity toward heat-induced denaturing and a lower Zn(2+) binding affinity. Glu(350) apparently occupies a central position in the active site and presumably positions His(222) and Arg(362).
Monoclonal antibodies for prophylaxis and therapy of infectious diseases (2007)

Monoclonal antibodies (mAb) are attractive biologic drugs due to their exquisite specificity and well understood mechanisms of action, which results in a higher predictability and lower attrition rate compared with other drugs. Therefore, it may seem surprising that only a single mAb is presently marketed for an infectious disease indication. However, the antibiotic resistance crisis, emerging viral diseases and bioterroristic threats have recently spurred the development of anti-infective mAbs, of which more than a dozen are being tested in clinical trials. Conceptually, and validated in many preclinical models, mAbs will be most effective when used prophylactically against acute viral infections and bacterial toxins. The acute bacterial and chronic viral infections, which are medically and economically far more important, are much more difficult to control by antibodies, as the recent clinical failure of some polyclonal antibody products has shown. In these situations, the synergistic action of two or more mAbs together with a small molecule drug will most likely be required for therapeutic efficacy. This review aims to highlight the scientific and economic opportunities and obstacles that are encountered in the quest to add mAbs to the armament of anti-infective drugs.
[Electrodiagnostic and histochemical studies on the effect of electric stimulation on the atrophy of denervated laryngeal muscles in animal experiments]. (1983)

1. The stimulation of denervated laryngeal muscles by external application of exponential current impulses is selective. 2. The extent of the neurogenous atrophy of denervated muscles following paralysis of the recurrent nerve can be diagnosed electrically. 3. This atrophy could be significantly reduced by proper choice of stimulation parameters within the time span of the experiment (28 days).
[Repair of rectovaginal fistula using pudendal-thigh flap pedicled on the obturator artery]. (2000)

The advantages of the pudendal-thigh flap pedicled on the obturator artery include: 1. Good blood supply; 2. Relative thin and hairless; 3. Perfect hiding of the donor site. We think that it is one of the best methods of rectovaginal fistula repair.
Uncoated, Broad Fluorescent, and Size-Homogeneous CdSe Quantum Dots for Bioanalyses (2005)

In the present study, we describe the synthesis of highly luminescent uncoated water-soluble CdSe quantum dots (QDs) possessing the following characteristics: approximately 2 nm in diameter, with very good size distribution (in 95% homodispersed) accompanied by a broad-band photoluminescent spectrum. The synthetic procedure is simple, is conducted at room temperature, in the absence of the most popular coordinating ligands (as TOPO or HDA), and is highly reproducible. The obtained CdSe core QDs possessed a comparatively long fluorescence half-life (approximately 30-90 ns, depending on the emission wavelength) detected by time-resolved spectroscopy. These QDs were further conjugated with antibodies and applied in several biochemical analyses.
Pharmacological potential of cerium oxide nanoparticles (2011)

Nanotechnology promises a revolution in pharmacology to improve or create ex novo therapies. Cerium oxide nanoparticles (nanoceria), well-known as catalysts, possess an astonishing pharmacological potential due to their antioxidant properties, deriving from a fraction of Ce(3+) ions present in CeO(2). These defects, compensated by oxygen vacancies, are enriched at the surface and therefore in nanosized particles. Reactions involving redox cycles between the Ce(3+) and Ce(4+) oxidation states allow nanoceria to react catalytically with superoxide and hydrogen peroxide, mimicking the behavior of two key antioxidant enzymes, superoxide dismutase and catalase, potentially abating all noxious intracellular reactive oxygen species (ROS) via a self-regenerating mechanism. Hence nanoceria, apparently well tolerated by the organism, might fight chronic inflammation and the pathologies associated with oxidative stress, which include cancer and neurodegeneration. Here we review the biological effects of nanoceria as they emerge from in vitro and in vivo studies, considering biocompatibility and the peculiar antioxidant mechanisms.
The Absorption Spectrum of Biphenylene (1941)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Absorption Spectrum of BiphenyleneEmma P. Carr, Lucy W. Pickett, and Dorothy VorisCite this: J. Am. Chem. Soc. 1941, 63, 11, 3231–3232Publication Date (Print):November 1, 1941Publication History Published online1 May 2002Published inissue 1 November 1941https://pubs.acs.org/doi/10.1021/ja01856a503https://doi.org/10.1021/ja01856a503research-articleACS PublicationsRequest reuse permissionsArticle Views106Altmetric-Citations13LEARN 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
A Phase II Multicenter Study of Visilizumab, Humanized Anti-CD3 Antibody, to Treat Steroid-Refractory Acute Graft-versus-Host Disease (2005)

Results of a previous phase I study suggested that a single 3 mg/m2 dose of the humanized non-FcR-binding anti-CD3 monoclonal antibody visilizumab (Nuvion) was well tolerated and had efficacy for the treatment of steroid-refractory acute graft-versus-host disease (GVHD). We now report results of a multicenter phase II study in which visilizumab was given to 44 participants with steroid-refractory acute GVHD. Eighty-two percent of the participants had visceral involvement, and 86% had overall grade III or IV acute GVHD at study entry. The respective complete and overall response rates were 14% and 32% at 42 days. Plasma Epstein-Barr virus DNA increased to more than 1000 copies per milliliter in 19 subjects. Seventeen received rituximab, and no fatal lymphoproliferative disorders were observed. Survival at 180 days was 32% (95% confidence interval, 18%-46%). The administration of visilizumab as used in this study seems to be sufficiently safe and effective to warrant further assessment for treatment or prevention of GVHD.
Demonstration by a Novel Genetic Technique That Leader Peptidase Is an Essential Enzyme of Escherichia coli (1983)

It was previously shown that two separate regions of DNA are required for expression of the cloned leader peptidase gene on plasmid pTD101 (T. Date and W. Wickner, Proc. Natl. Acad. Sci. U.S.A. 78:6106-6110, 1981). Both loci have been mapped in detail, and their roles have been established. A 1.3-kilobase region, termed the L region, encodes the 37,000-dalton leader peptidase protein. Another region, termed the P region, is about 1.5 kilobases away from the L region and is less than 350 base pairs long. The P region acts in cis to the L region, suggesting that it plays a role as a promoter. A technique for inactivation of the leader peptidase gene on the Escherichia coli chromosome has been developed to examine whether the leader peptidase which we had cloned is essential for cell growth. A specific plasmid (P(-) L(-)) which deletes both the P region and a substantial portion of the L region was constructed and transformed into a polA mutant strain. The plasmid cannot replicate in this strain; thus, the plasmid-borne ampicillin resistance is lost unless the plasmid DNA recombines into the chromosome. Integration of the P(-) L(-) plasmid did not yield any viable ampicillin-resistant cells, whereas the three control plasmids, P(+) L(+), P(+) L(-), and P(-) L(+), did. When the P(-) L(-) plasmid was transformed into the polA(Ts) strain, the strain could only grow in the presence of ampicillin at a permissive temperature, suggesting that integration of the plasmid into the host chromosome leads to inactivation of the chromosomal leader peptidase gene. Southern hybridization analysis demonstrated that the integration of plasmids into the chromosome occurred at the homologous site. This study demonstrates that expression of the leader peptidase gene is critical for cell growth.
Review article: adherence to medication for chronic hepatitis C – building on the model of human immunodeficiency virus antiretroviral adherence research (2009)

As HCV treatment becomes more complex with new classes of agents, adherence will be increasingly important to treatment success as resistance mutations may develop with suboptimal dosing of HCV enzyme inhibitors. HIV adherence research can be applied to that on HCV to establish accurate methods to assess adherence, investigate determinants of non-adherence and develop strategies to optimize adherence.
Treatment of Adult T-Cell Leukemia–Lymphoma with a Combination of Interferon Alfa and Zidovudine (1995)

The combination of zidovudine and interferon alfa has activity against adult T-cell leukemia-lymphoma, even in patients in whom prior cytotoxic therapy has failed. This regimen should be evaluated further for its role in the treatment of adult T-cell leukemia-lymphoma.
Brentuximab vedotin (2012)

Brentuximab vedotin (SGN-35; Adcetris®) is an anti-CD30 antibody conjugated via a protease-cleavable linker to the potent anti-microtubule agent monomethyl auristatin E (MMAE). Following binding to CD30, brentuximab vedotin is rapidly internalized and transported to lysosomes where MMAE is released and binds to tubulin, leading to cell cycle arrest and apoptosis. Several trials have shown durable antitumor activity with a manageable safety profile in patients with relapsed/refractory Hodgkin lymphoma, systemic anaplastic large cell lymphoma, or primary cutaneous CD30-positive lymphoproliferative disorders. Peripheral sensory neuropathy is a significant adverse event associated with brentuximab vedotin administration. Neuropathy symptoms are cumulative and dose-related. Multiple ongoing trials are currently evaluating brentuximab vedotin alone or in combination with other agents in relapsed/refractory patients, as well as patients with newly diagnosed disease.
Characterization of Leptospiral Outer Membrane Lipoprotein LipL36: Downregulation Associated with Late-Log-Phase Growth and Mammalian Infection (1998)

We report the cloning of the gene encoding a 36-kDa leptospiral outer membrane lipoprotein, designated LipL36. We obtained the N-terminal amino acid sequence of a staphylococcal V8 proteolytic-digest fragment in order to design an oligonucleotide probe. A Lambda-Zap II library containing EcoRI fragments of Leptospira kirschneri DNA was screened, and a 2.3-kb DNA fragment which contained the entire structural lipL36 gene was identified. Several lines of evidence indicate that LipL36 is lipid modified in a manner similar to that of LipL41, a leptospiral outer membrane lipoprotein we described in a previous study (E. S. Shang, T. A. Summers, and D. A. Haake, Infect. Immun. 64:2322-2330, 1996). The deduced amino acid sequence of LipL36 would constitute a 364-amino-acid polypeptide with a 20-amino-acid signal peptide, followed by an L-X-Y-C lipoprotein signal peptidase cleavage site. LipL36 is solubilized by Triton X-114 extraction of L. kirschneri; phase separation results in partitioning of LipL36 exclusively into the hydrophobic, detergent phase. LipL36 is intrinsically labeled during incubation of L. kirschneri in media containing [3H]palmitate. Processing of LipL36 is inhibited by globomycin, a selective inhibitor of lipoprotein signal peptidase. After processing, LipL36 is exported to the outer membrane along with LipL41 and lipopolysaccharide. Unlike LipL41, there appears to be differential expression of LipL36. In early-log-phase cultures, LipL36 is one of the most abundant L. kirschneri proteins. However, LipL36 levels drop considerably beginning in mid-log phase. LipL36 expression in vivo was evaluated by examining the humoral immune response to leptospiral antigens in the hamster model of leptospirosis. Hamsters surviving challenge with culture-adapted virulent L. kirschneri generate a strong antibody response to LipL36. In contrast, sera from hamsters surviving challenge with host-adapted L. kirschneri do not recognize LipL36. These findings suggest that LipL36 expression is downregulated during mammalian infection, providing a marker for studying the mechanisms by which pathogenic Leptospira species adapt to the host environment.
Inhibition of Hypoxia-inducible Factor 1 Activation by Carbon Monoxide and Nitric Oxide (1999)

It has been proposed that cells sense hypoxia by a heme protein, which transmits a signal that activates the heterodimeric transcription factor hypoxia-inducible factor 1 (HIF-1), thereby inducing a number of physiologically relevant genes such as erythropoietin (Epo). We have investigated the mechanism by which two heme-binding ligands, carbon monoxide and nitric oxide, affect oxygen sensing and signaling. Two concentrations of CO (10 and 80%) suppressed the activation of HIF-1 and induction of Epo mRNA by hypoxia in a dose-dependent manner. In contrast, CO had no effect on the induction of HIF-1 activity and Epo expression by either cobalt chloride or the iron chelator desferrioxamine. The affinity of CO for the putative sensor was much lower than that of oxygen (Haldane coefficient, approximately 0.5). Parallel experiments were done with 100 microM sodium nitroprusside, a nitric oxide donor. Both NO and CO inhibited HIF-1 DNA binding by abrogating hypoxia-induced accumulation of HIF-1alpha protein. Moreover, both NO and CO specifically targeted the internal oxygen-dependent degradation domain of HIF-1alpha, and also repressed the C-terminal transactivation domain of HIF-1alpha. Thus, NO and CO act proximally, presumably as heme ligands binding to the oxygen sensor, whereas desferrioxamine and perhaps cobalt appear to act at a site downstream.
Pathway-based drug repositioning using causal inference (2013)

We successfully developed a computational method for discovering new uses of existing drugs based on casual inference in a layered drug-target-pathway-gene- disease network. The results showed that our proposed method enables hypothesis generation from public accessible biological data for drug repositioning.
Direct Comparison of the Insulating Properties of Two Genetic Elements in an Adenoviral Vector Containing Two Different Expression Cassettes (2004)

Targeted gene expression can be achieved through the use of cell-selective promoters. However, when the expression cassette is delivered by an adenovirus, "promoter interference," resulting in the loss of specificity, has been reported. To overcome this problem, insulator elements (the bovine growth hormone transcription stop signal or HS4 chromatin insulators of the chicken beta-globin locus) have been used. The present study examines the efficacy of these insulators elements, when two independent expression cassettes (one in which a strong, ubiquitous promoter drives the expression of the green fluorescent protein and another in which the "cancer-selective" ERBB2 promoter drives the expression of the herpes simplex virus thymidine kinase [HSVtk] gene) are incorporated into the same recombinant adenovirus. As expected, the presence of either insulator does not alter the expression of HSVtk in ERBB2-positive cells, measured through sensitization of the cells to ganciclovir. When ERBB2-negative cells were infected at a multiplicity of infection (MOI) of 10, the uninsulated virus sensitized ERBB2-negative cells to the same extent as it did for ERBB2-positive cells; partial sensitization was observed when transcriptional terminators were used, indicating a partial insulating effect; and complete insulation (no sensitization to ganciclovir) was observed when HS4 chromatin insulators were used. However, this complete insulation was lost when the MOI of virus was increased to 100. Our study demonstrates the possibility of insulating a conditionally expressed transgene in the vicinity of another expression cassette, but this insulating effect is lost when the multiplicity of infection is increased.
Heterotrophic Growth of Two Strains of the Acido-Thermophilic Red Alga <italic>Galdieria sulphuraria</italic> (1995)

Journal Article Heterotrophic Growth of Two Strains of the Acido-Thermophilic Red Alga Galdieria sulphuraria Get access Wolfgang Gross, Wolfgang Gross Institut für Pflanzenphysiologie and MikrobiologieKönigin-Luise-Str. 12-16a, 14195 Berlin, FR Germany Search for other works by this author on: Oxford Academic Google Scholar Claus Schnarrenberger Claus Schnarrenberger Institut für Pflanzenphysiologie and MikrobiologieKönigin-Luise-Str. 12-16a, 14195 Berlin, FR Germany Search for other works by this author on: Oxford Academic Google Scholar Plant and Cell Physiology, Volume 36, Issue 4, June 1995, Pages 633–638, https://doi.org/10.1093/oxfordjournals.pcp.a078803 Published: 01 June 1995 Article history Received: 21 November 1994 Accepted: 09 March 1995 Published: 01 June 1995
A Direct Transposon Insertion Tool for Modification and Functional Analysis of Viral Genomes (2002)

ABSTRACT Advances in DNA transposition technology have recently generated efficient tools for various types of functional genetic analyses. We demonstrate here the power of the bacteriophage Mu-derived in vitro DNA transposition system for modification and functional characterization of a complete bacterial virus genome. The linear double-stranded DNA genome of Escherichia coli bacteriophage PRD1 was studied by insertion mutagenesis with reporter mini-Mu transposons that were integrated in vitro into isolated genomic DNA. After introduction into bacterial cells by electroporation, recombinant transposon-containing virus clones were identified by autoradiography or visual blue-white screening employing α-complementation of E. coli β-galactosidase. Additionally, a modified transposon with engineered Not I sites at both ends was used to introduce novel restriction sites into the phage genome. Analysis of the transposon integration sites in the genomes of viable recombinant phage generated a functional map, collectively indicating genes and genomic regions essential and nonessential for virus propagation. Moreover, promoterless transposons defined the direction of transcription within several insert-tolerant genomic regions. These strategies for the analysis of viral genomes are of a general nature and therefore may be applied to functional genomics studies in all prokaryotic and eukaryotic cell viruses.