gebhart/patrepeval huggingface dataset:
Strand Specificity of Nicking of DNA at Chi Sites by RecBCD Enzyme (1995)

RecBCD enzyme is essential for the major pathway of homologous recombination of linear DNA in Escherichia coli. It is a potent nuclease and helicase and, during its unwinding of double-stranded DNA, makes single-strand scissions in the vicinity of Chi recombination hot spots. We report here that both the strand that is cut and the position of the cuts relative to Chi depended on the ATP to Mg2+ ratio. With ATP in excess, Chi-dependent nicks occurred, as we have previously reported, four to six nucleotides to the 3'-side of the Chi octamer (5'-GCTGGTGG-3') and were detected only on the strand bearing that sequence. Three differences were seen with Mg2+ in excess. 1) Chi-dependent 3'-ends were produced on the GCTGGTGG-containing strand closer to and within the Chi octamer. 2) Chi-dependent cuts occurred on the complementary DNA strand. 3) RecBCD enzyme destroyed the 3'-terminated strand of DNA from its entry point up to the vicinity of the Chi site, as others have previously reported. We show here that, with Mg2+ in excess, the enzyme continued to travel along DNA, after encountering a Chi site, releasing both strands of the DNA distal to Chi as single strands. We discuss potential biological consequences of these two modes of RecBCD enzyme-Chi interaction.
Influence of Surface States on Electron Transport through Intrinsic Ge Nanowires (2005)

Solution-grown single-crystal Ge nanowires were used as conductive channels in field effect transistor devices to study the influence of surface states on their electron transport properties. Nanowires contacted with Pt electrodes using focused ion beam metal deposition exhibited linear current-voltage (IV) curves at room temperature with apparent resistivities ranging from 10(1) to 10(-1) Omega cm. In all cases, the nanowire conductance decreased with positive external electric fields applied perpendicular to the nanowire surface by a gate electrode, characteristic of p-type carrier accumulation at the nanowire surface. The field-induced change in conductance exhibited a time-dependent relaxation, with response time and magnitude of current decrease that depended on the nanowire surface chemistry. Nanowires treated with an organic passivation layer using a thermally initiated hydrogermylation reaction exhibited 2 orders of magnitude slower current relaxation and a smaller decrease in current relative to "bare" nanowires with oxidized surfaces.
Fermented cereal beverages: from probiotic, prebiotic and synbiotic towards Nanoscience designed healthy drinks (2017)

There is currently a great interest in producing healthy food in particular that which has an impact in improving the gastrointestinal health such as probiotics, prebiotics and synbiotics. Most of these functional foods are dairy based and have been greatly accepted worldwide. Nevertheless, there has been a need for the development of nondairy probiotic, prebiotic and synbiotic products. This has encouraged food scientists to study the feasibility of applying other fermenting substrates such as cereals for the development of innovative nondairy fermented functional foods. Therefore, in this review we have addressed the significance of applying cereals and their fractions for the development of probiotic, prebiotic and synbiotic beverages. Furthermore, we have presented the importance of including nanoscience and nanotechnology techniques for the creation of fermented cereal beverages that contain specific bioactive nanoparticles. Thus, this work provides the guidelines to promote the development of novel nano-designed fermented cereal beverages that could significantly have an impact on the health of the consumers.
<title>Signal Processing Aspects Of The S-1 Multiprocessor Project</title> (1980)

The S-1 family of uni-and multiprocessors is an extremely high performance but relatively inexpen-sive general purpose set of digital processing systems being developed for the most demanding National security applications. A typical S-1 system consists of from one to sixteen S-1 uniprocessors sharing up to 4 gigawords of uniformly addressed main memory. Each uniprocessor of the current (Mark IIA) generation has computational power roughly equivalent to that of a CRAY-1. In this paper, we give a general description of the S-1 Mark IIA uniprocessor and a somewhat more extensive discussion of its signal processing hardware and hardware-executed algorithms. Our focus is a discussion of the felicitous properties of the uniprocessor components that make the S-1 system a powerful general purpose digital signal processor.
Atomoxetine Also Effective in Patients Suffering From Narcolepsy? (2005)

THE ABSENCE OF HYPOTHALAMIC hypocretin-containing neurons. The pathophysiology of the disorder is still unknown but an imbalance between monoamines and acetylcholine is generally accepted. Narcolepsy is characterized by chronic excessive sleepiness that significantly impairs daily life. Narcoleptic symptoms interfere with participation in interpersonal and social activities. Disease onset occurred abruptly with excessive sleepiness and irresistible naps during the day. Two months previously he was perfectly awake under the same conditions. No triggering factors or accompanying symptoms could be identified except for increased appetite and substantial weight gain (10 kg over the last year). The patient fell asleep regularly at work and was found napping at home. Clear-cut cataplexy with bilateral muscle weakness in lower limbs and face muscles, having duration of a few seconds with daily episodes and injurious falls, triggered by laughter, subsequently appeared. The history was considered typical for classical narcolepsy cataplexy, in the absence of sleep paralysis or hallucinations. Neurologic and psychiatric examinations were normal. Family history was negative for sleep or neurologic disorders. A routine EEG was normal, with the absence of epileptiform activities or signs of sleepiness. Standard brain magnetic resonance imaging did not reveal any lesion. After obtaining informed consent we initiated Atomoxetine 40mg TID for 4 consecutive weeks. Six days after start of treatment, improvement of both sleepiness and cataplexy were noticed. In the following 3 weeks only 2 attacks of cataplexy or irresistible nap were reported. The patient reported a significant improvement' of his chronic escessive sleepiness. After 4 weeks the treatment was stopped and Modafinil at 200 mg/day was instituted. At the time of the last interview with the patient, no reappearance of cataplectic attacks, with few leading to falls, was reported. This is the first report, to my knowledge, illustrating the clinical efficacy of Atomoxetine, a highly selective noradrenaline reuptake inhibitor, after the onset of first narcolepsy symptoms. If confirmed in controlled trials and with objective measures of sleepiness, this finding suggests a good efficacy of Atomoxetine also for narcolepsy.
Gene Repair and Transposon‐Mediated Gene Therapy (2002)

The main strategy of gene therapy has traditionally been focused on gene augmentation. This approach typically involves the introduction of an expression system designed to express a specific protein in the transfected cell. Both the basic and clinical sciences have generated enough information to suggest that gene therapy would eventually alter the fundamental practice of modern medicine. However, despite progress in the field, widespread clinical applications and success have not been achieved. The myriad deficiencies associated with gene augmentation have resulted in the development of alternative approaches to treat inherited and acquired genetic disorders. One, derived primarily from the pioneering work of homologous recombination, is gene repair. Simply stated, the process involves targeting the mutation in situ for gene correction and a return to normal gene function. Site-specific genetic repair has many advantages over augmentation although it too is associated with significant limitations. This review outlines the advantages and disadvantages of gene correction. In particular, we discuss technologies based on chimeric RNA/DNA oligonucleotides, single-stranded and triplex-forming oligonucleotides, and small fragment homologous replacement. While each of these approaches is different, they all share a number of common characteristics, including the need for efficient delivery of nucleic acids to the nucleus. In addition, we review the potential application of a novel and exciting nonviral gene augmentation strategy--the Sleeping Beauty transposon system.
The role of the B7-1a molecule, an alternatively spliced form of murine B7-1 (CD80), on T cell activation (1996)

B7 molecules (CD80 (B7-1) and CD86 (B7-2/B70)) on APCs provide costimulatory signals for T cell proliferation. We previously described the presence of an alternatively spliced form of murine CD80 (previously termed MB7-2 and renamed as B7-1a) that completely lacks the second Ig-like domain coded by exon 3 in activated murine B cells. in this study, we first examined whether B7-1a mRNA can be detected in vivo by RNase protection assay. The expression of B7-1a mRNA was only detected in lymphoid organs although the level of expression was lesser than that of CD80 mRNA. However, we demonstrated that the expression of B7-1a mRNA like CD80 mRNA was considerably augmented in spleen cells treated with either LPS in vitro or OVA/CFA conjugate in vivo. We next determined the functional activity of B7-1a using Chinese hamster ovary (CHO) cells transfected by B7 genes. When resting T cells were cocultured with CHO cells expressing B7-1a molecules in the presence of PMA/ionomycin, T cell proliferation was not detected, while CHO cells either expressing CD80 or CD86 could promote the proliferation of resting T cells. in contrast to resting T cells, CHO cells expressing B7-1a could support the proliferation of activated T cells. Thus, costimulatory activity of B7-1a molecules was dependent upon the activation stage of T cells. Therefore the IgV-like region of CD80 contains a critical region for functional interaction with its ligands and can transduce a costimulatory signal for T cell proliferation.
Development of Unimolecular Tetrakis(piperidin‐4‐ol) as a Ligand for Suzuki–Miyaura Cross‐Coupling Reactions: Synthesis of Incrustoporin and Preclamol (2015)

Abstract A domino aza‐Cope/aza‐Prins cascade enabled the synthesis of a new class of 4‐hydroxypiperidine‐appended mono, bis, tris, and tetrakis unimolecular compounds that served as efficient ligands to catalyze Suzuki–Miyaura cross‐coupling reactions under aerobic conditions. Various biaryls, terphenyls, and heterocyclic biphenyls were obtained in good to excellent yields. The ligands were also capable of catalyzing the Heck–Mizoroki reaction. As an application, the Suzuki–Miyaura coupling reaction was used in the synthesis of incrustoporin, its analogs, and the drug molecule preclamol.
The three bellies of the canine posterior cricoarytenoid muscle: Implications for understanding laryngeal function (1993)

The posterior cricoarytenoid (PCA) muscle is known to be active during phonation and respiration. The presence of muscle compartments (bellies) that might subserve these functions was investigated in the canine PCA by anatomical dissection and muscle fiber histochemistry. Five PCA muscles were microdissected and the origins and insertions of all muscle bundles were recorded. An additional six PCA muscles were frozen, sectioned, and stained for adenosine triphosphatase (ATPase) activity. The total number of fast- and slow-twitch fibers were counted and their proportion was determined for each region of the muscle. The PCA muscle was found to contain three distinct neuromuscular compartments. The vertical compartment is oriented at 24 degrees from true vertical, inserts on the lateral aspect of the muscular process of the arytenoid, and is composed of 65% type 2 (fast) muscle fibers. The oblique is oriented at 44 degrees from vertical, inserts on the top of the muscular process of the arytenoid, and is composed of 77% type 2 muscle fibers. The horizontal is oriented at 63 degrees from vertical, inserts on the medial aspect of the muscular process of the arytenoid, and is composed of 59% type 2 muscle fibers. The cricoarytenoid joint is capable of three arcs of motion and the physical arrangement of each compartment appears to correspond to each of these motions. Moreover, the histochemical profiles show that the activity of the three bellies is quite different. These results suggest that the different compartments of the PCA perform distinctive motions during phonation and inspiration.
Asymmetric Aldol Route to Hydroxyethylamine Isostere:  Stereoselective Synthesis of the Core Unit of Saquinavir (1997)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTAsymmetric Aldol Route to Hydroxyethylamine Isostere: Stereoselective Synthesis of the Core Unit of SaquinavirArun K. Ghosh, Khaja Azhar Hussain, and Steve FidanzeView Author Information Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607Cite this: J. Org. Chem. 1997, 62, 17, 6080–6082Publication Date (Web):August 22, 1997Publication History Received17 April 1997Published online22 August 1997Published inissue 1 August 1997https://pubs.acs.org/doi/10.1021/jo9706943https://doi.org/10.1021/jo9706943brief-reportACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views586Altmetric-Citations32LEARN 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 SUBJECTS:Enantioselective synthesis,Ethers,Inhibitors,Peptides and proteins,Substituents Get e-Alerts
Severe Zinc Depletion of Escherichia coli (2009)

Zinc ions play indispensable roles in biological chemistry. However, bacteria have an impressive ability to acquire Zn(2+) from the environment, making it exceptionally difficult to achieve Zn(2+) deficiency, and so a comprehensive understanding of the importance of Zn(2+) has not been attained. Reduction of the Zn(2+) content of Escherichia coli growth medium to 60 nm or less is reported here for the first time, without recourse to chelators of poor specificity. Cells grown in Zn(2+)-deficient medium had a reduced growth rate and contained up to five times less cellular Zn(2+). To understand global responses to Zn(2+) deficiency, microarray analysis was conducted of cells grown under Zn(2+)-replete and Zn(2+)-depleted conditions in chemostat cultures. Nine genes were up-regulated more than 2-fold (p < 0.05) in cells from Zn(2+)-deficient chemostats, including zinT (yodA). zinT is shown to be regulated by Zur (zinc uptake regulator). A mutant lacking zinT displayed a growth defect and a 3-fold lowered cellular Zn(2+) level under Zn(2+) limitation. The purified ZinT protein possessed a single, high affinity metal-binding site that can accommodate Zn(2+) or Cd(2+). A further up-regulated gene, ykgM, is believed to encode a non-Zn(2+) finger-containing paralogue of the Zn(2+) finger ribosomal protein L31. The gene encoding the periplasmic Zn(2+)-binding protein znuA showed increased expression. During both batch and chemostat growth, cells "found" more Zn(2+) than was originally added to the culture, presumably because of leaching from the culture vessel. Zn(2+) elimination is shown to be a more precise method of depleting Zn(2+) than by using the chelator N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine.
Nod2 Mutation in Crohn's Disease Potentiates NF-κB Activity and IL-1ß Processing (2005)

Variants of NOD2, an intracellular sensor of bacteria-derived muramyl dipeptide (MDP), increase susceptibility to Crohn's disease (CD). These variants are thought to be defective in activation of nuclear factor kappaB (NF-kappaB) and antibacterial defenses, but CD clinical specimens display elevated NF-kappaB activity. To illuminate the pathophysiological function of NOD2, we introduced such a variant to the mouse Nod2 locus. Mutant mice exhibited elevated NF-kappaB activation in response to MDP and more efficient processing and secretion of the cytokine interleukin-1beta (IL-1beta). These effects are linked to increased susceptibility to bacterial-induced intestinal inflammation and identify NOD2 as a positive regulator of NF-kappaB activation and IL-1beta secretion.
High-Speed Free-Flow Electrophoresis on Chip (2003)

A microfluidic device has been developed for continuous separation in free-flow electrophoresis (FFE) mode. A mixture of two fluorescent reagents is separated into two component streams in 75 ms using a sample flow rate of 2 nL/s. The residence time of sample in the whole separation compartment is 2 s. The separation bed volume is 0.2 microL. The chip has also been used for free-flow electrophoresis of fluorescein-5-isothiocyanate-labeled amino acids in both aqueous and binary media. The short residence time and small sample flow rate make the FFE chip feasible for on-line monitoring on production lines and other chemical or biochemical processes. The in-house-made chip was composed of a plain glass substrate of 1.5-mm thickness and a PDMS layer of 0.3-mm thickness with micromachined channels. The channel design presented in this paper is versatile. With the same kind of PDMS substrates, chips for various purposes can be made depending on the locations of the reservoirs, which are cut out on the PDMS substrate. The results presented verify the scaling laws and allow prediction of FFE performances comparable to what is now state of the art on capillary electrophoresis chips.
Pharmacokinetics of trimetrexate administered by five-day continuous infusion to patients with advanced cancer. (1987)

The disposition of the methotrexate analogue trimetrexate (TMTX, NSC 352122; 2,4-diammino-5-methyl-6-[(3,4,5-trimethoxyanilino)methyl]qui nazoline) was determined in a Phase I study in 16 patients with refractory or relapsing cancer. The drug was administered by continuous 5-day infusion at doses of 5 to 60 mg/m2/120 h (1-12 mg/m2 daily for 5 days). Plasma and urine collections were made during and after infusion and TMTX levels were quantitated by a specific and sensitive high-performance liquid chromatographic assay. Estimates of pharmacokinetic parameters were similar when determined by either compartmental or noncompartmental methods. There were no significant differences in parameters between the first and second courses of treatment to 10 of the patients. Significant linear relations between TMTX dose and the area under curve of plasma TMTX (r2 = 0.858, P = 0.0001) and the steady-state TMTX plasma level (r2 = 0.764, P = 0.0001) were established. Total TMTX clearance was 30.4 +/- 7.6 (SD) ml/min/m2, renal clearance 7.80 +/- 3.9 ml/min/m2, nonrenal clearance 23.2 +/- 7.1 ml/min/m2, volume of distribution 32.8 +/- 16.6 liters/m2, and terminal half-life 13.4 +/- 7.0 h. The percentage of the trimetrexate dose excreted unchanged in urine ranged from 8.4 to 40.7% (mean, 24.9 +/- 9.2%) and was related to creatinine clearance (r2 = 0.312, P = 0.010). Trimetrexate renal clearance was also related to urine flow (r2 = 0.330, P = 0.008). Trimetrexate pharmacokinetics was linear over the dose range 5 to 60 mg/m2 when given by 5-day continuous infusion to patients but there was evidence of urine flow-dependent renal clearance which requires further examination.
Inhibition of hydroxycinnamic acid sulfation by flavonoids and their conjugated metabolites (2013)

Hydroxycinnamic acids and flavonoids are dietary phenolic antioxidants that are abundant in our diet. Hydroxycinnamic acids are highly sulfated in vivo, and sulfotransferases (SULTs), in particular SULT1A1, play a major role in their metabolism. Flavonoids are potent inhibitors of human SULTs. In this study, the potential metabolic interaction between dietary hydroxycinnamic acids and flavonoids was investigated. Flavonoids, such as luteolin, quercetin, daidzein, and genistein, are identified as potent inhibitors of hydroxycinnamic acid sulfation in human liver S9 homogenate with IC50 values <1 µM. The inhibitory activity was less potent in the human intestinal S9 homogenate. We also demonstrate that quercetin conjugates found in vivo (quercetin-3-O-glucuronide, quercetin-7-O-glucuronide, and quercetin-3'-O-sulfate) moderately inhibited the sulfation of hydroxycinnamic acids in human liver S9. In an intact cellular system, human HepG2 cells, caffeic acid and ferulic acid sulfation was inhibited by luteolin and quercetin (IC50 : 1.6-3.9 µM). Quercetin-3'-O-sulfate weakly inhibited sulfation. Quercetin glucuronides, limited by their low cellular uptake, were ineffective. These data suggest that the inhibition of SULTs by flavonoids and in vivo flavonoid conjugates may modify the bioavailability of dietary hydroxycinnamic acids by suppressing their conversion to sulfated metabolites.
Molecular cloning and characterization of the cDNA coding for C4b-binding protein, a regulatory protein of the classical pathway of the human complement system (1985)

By using synthetic oligonucleotides as probes, plasmid clones containing portions of cDNA coding for human C4b-binding protein were isolated from a liver cDNA library. The entire amino acid sequence of the C4b-binding protein can be predicted from this study of the cloned cDNA when allied to a previous sequence study at the protein level [Chung, Gagnon & Reid (1985) Mol. Immunol. 22, 427-435], in which over 55% of the amino acid sequence, including the N-terminal 62 residues, was obtained. The plasmid clones isolated allowed the unambiguous determination of 1717 nucleotides of cDNA sequence between the codon for the 32nd amino acid in the sequence of C4b-binding protein and the 164th nucleotide in the 3' non-translated region. The sequence studies show that the secreted form of C4b-binding protein, found in plasma, is composed of chains of apparent Mr 70 000 that contains 549 amino acid residues. Examination of the protein and cDNA sequence results show that there are at least two polymorphic sites in the molecule. One is at position 44, which can be glutamine or threonine, and the other is at position 309, which can be tyrosine or histidine. Northern-blot analysis indicated that the mRNA for C4b-binding protein is approx. 2.5 kilobases long. The N-terminal 491 amino acids of C4b-binding protein can be divided into eight internal homologous regions, each approx. 60 amino acids long, which can be aligned by the presence in each region of four half-cystine, one tryptophan and several other conserved residues. These regions in C4b-binding protein are homologous with the three internal-homology regions that have been reported to be present within the Ba region of the complement enzyme factor B and also to the internal-homology regions found in the non-complement beta 2-glycoprotein I.