gebhart/patrepeval huggingface dataset:
Rapid Antimicrobial Susceptibility Testing by Sensitive Detection of Precursor rRNA Using a Novel Electrochemical Biosensing Platform (2012)

Precursor rRNA (pre-rRNA) is an intermediate stage in the formation of mature rRNA and is a useful marker for cellular metabolism and growth rate. We developed an electrochemical sensor assay for Escherichia coli pre-rRNA involving hybridization of capture and detector probes with tail sections that are spliced away during rRNA maturation. A ternary self-assembled monolayer (SAM) prepared on gold electrode surfaces by coassembly of thiolated capture probes with hexanedithiol and posttreatment with 6-mercapto-1-hexanol minimized the background signal and maximized the signal-to-noise ratio. Inclusion of internal calibration controls allowed accurate estimation of the pre-rRNA copy number per cell. As expected, the ratio of pre-rRNA to mature rRNA was low during stationary phase and high during log phase. Pre-rRNA levels were highly dynamic, ranging from 2 copies per cell during stationary phase to ~1,200 copies per cell within 60 min of inoculation into fresh growth medium. Specificity of the assay for pre-rRNA was validated using rifampin and chloramphenicol, which are known inhibitors of pre-rRNA synthesis and processing, respectively. The DNA gyrase inhibitor, ciprofloxacin, was found to act similarly to rifampin; a decline in pre-rRNA was detectable within 15 min in ciprofloxacin-susceptible bacteria. Assays for pre-rRNA provide insight into cellular metabolism and are promising predictors of antibiotic susceptibility.
High-Performance Multifunctional Graphene Yarns: Toward Wearable All-Carbon Energy Storage Textiles (2014)

The successful commercialization of smart wearable garments is hindered by the lack of fully integrated carbon-based energy storage devices into smart wearables. Since electrodes are the active components that determine the performance of energy storage systems, it is important to rationally design and engineer hierarchical architectures atboth the nano- and macroscale that can enjoy all of the necessary requirements for a perfect electrode. Here we demonstrate a large-scale flexible fabrication of highly porous high-performance multifunctional graphene oxide (GO) and rGO fibers and yarns by taking advantage of the intrinsic soft self-assembly behavior of ultralarge graphene oxide liquid crystalline dispersions. The produced yarns, which are the only practical form of these architectures for real-life device applications, were found to be mechanically robust (Young's modulus in excess of 29 GPa) and exhibited high native electrical conductivity (2508 ± 632 S m(-1)) and exceptionally high specific surface area (2605 m(2) g(-1) before reduction and 2210 m(2) g(-1) after reduction). Furthermore, the highly porous nature of these architectures enabled us to translate the superior electrochemical properties of individual graphene sheets into practical everyday use devices with complex geometrical architectures. The as-prepared final architectures exhibited an open network structure with a continuous ion transport network, resulting in unrivaled charge storage capacity (409 F g(-1) at 1 A g(-1)) and rate capability (56 F g(-1) at 100 A g(-1)) while maintaining their strong flexible nature.
Dead or Alive: Molecular Assessment of Microbial Viability (2014)

Nucleic acid-based analytical methods, ranging from species-targeted PCRs to metagenomics, have greatly expanded our understanding of microbiological diversity in natural samples. However, these methods provide only limited information on the activities and physiological states of microorganisms in samples. Even the most fundamental physiological state, viability, cannot be assessed cross-sectionally by standard DNA-targeted methods such as PCR. New PCR-based strategies, collectively called molecular viability analyses, have been developed that differentiate nucleic acids associated with viable cells from those associated with inactivated cells. In order to maximize the utility of these methods and to correctly interpret results, it is necessary to consider the physiological diversity of life and death in the microbial world. This article reviews molecular viability analysis in that context and discusses future opportunities for these strategies in genetic, metagenomic, and single-cell microbiology.
Development and Validation of the Premenstrual Symptoms Impact Survey (PMSIS): A Disease-Specific Quality of Life Assessment Tool (2008)

These results demonstrate that the PMSIS has excellent discriminative ability to detect differences in groups that are known to differ in terms of clinical criteria. The PMSIS can be used to educate consumers about the impact of their symptoms on QOL.
Organogel formation and molecular imprinting by functionalized gluconamides and their metal complexes (1997)

Functionalized gluconamides and their metal complexes are shown to give supramolecular assemblies, in some cases chiral, and to form organogels in a large variety of organic solvents, e.g. methacrylate mixtures which can be polymerized, as well as o-xylene, chloroform, ethyl acetate, ethanol and tetrahydrofuran.
DSIF, a novel transcription elongation factor that regulates RNA polymerase II processivity, is composed of human Spt4 and Spt5 homologs (1998)

We report the identification of a transcription elongation factor from HeLa cell nuclear extracts that causes pausing of RNA polymerase II (Pol II) in conjunction with the transcription inhibitor 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB). This factor, termed DRB sensitivity-inducing factor (DSIF), is also required for transcription inhibition by H8. DSIF has been purified and is composed of 160-kD (p160) and 14-kD (p14) subunits. Isolation of a cDNA encoding DSIF p160 shows it to be a homolog of the Saccharomyces cerevisiae transcription factor Spt5. Recombinant Supt4h protein, the human homolog of yeast Spt4, is functionally equivalent to DSIF p14, indicating that DSIF is composed of the human homologs of Spt4 and Spt5. In addition to its negative role in elongation, DSIF is able to stimulate the rate of elongation by RNA Pol II in a reaction containing limiting concentrations of ribonucleoside triphosphates. A role for DSIF in transcription elongation is further supported by the fact that p160 has a region homologous to the bacterial elongation factor NusG. The combination of biochemical studies on DSIF and genetic analysis of Spt4 and Spt5 in yeast, also in this issue, indicates that DSIF associates with RNA Pol II and regulates its processivity in vitro and in vivo.
Potential anti-inflammatory effects of 5-lipoxygenase inhibition--exemplified by the leukotriene synthesis inhibitor BAY X 1005. (1997)

Leukotrienes have been identified in various pathophysiologies. The leukotrienes LTB4 and LTC4 are assigned to inflammation. 5-lipoxygenase inhibitors which inhibit the synthesis of LTA4 being the precursor of both LTB4 and LTC4 appear to have only a limited antiinflammatory potential. 5-lipoxygenase inhibitors are represented by direct and indirect inhibitors, the latter competing with substrate transfer from the five-lipoxygenase activating protein (FLAP) to the 5-lipoxygenase enzyme. 5-lipoxygenase inhibition under experimental condition results in inhibition of edema formation, neutrophil infiltration, smooth muscle contraction after antigen challenge and prevention of early and late allergic reactions. Only in the cysteinyl-leukotriene-driven pathophysiology of allergic asthma and allergic rhinitis 5-lipoxygenase inhibition appears to provide symptomatic relief. Yet, the overall-antiinflammatory effect in man in far less than expected, but may be outweighed by the nearly total lack of any side effects of 5-lipoxygenase inhibition per se.
Ectocytosis caused by sublytic autologous complement attack on human neutrophils. The sorting of endogenous plasma-membrane proteins and lipids into shed vesicles (1991)

During sublytic complement attack on human neutrophils, plasma-membrane vesicles are shed from the cell surface as a cell-protection mechanism. By using surface-iodinated neutrophils it was found that less than 2% of surface label was recovered in shed vesicles under conditions where 40% of complement component C9 was shed. SDS/PAGE of 125I-labelled shed vesicles and plasma membranes showed differences in iodination pattern, demonstrating the sorting of membrane proteins into the shed vesicles. Analysis of 32P-labelled phospholipids after labeling of neutrophils with [32P]Pi before sublytic complement attack showed the presence of phosphatidic acid, phosphatidylcholine, phosphatidyl-ethanolamine, phosphatidylinositol and polyphosphoinositides in shed vesicles. Quantitative analysis using [3H]acetic anhydride-labelling method showed that the molar proportions of phosphatidylethanolamine, phosphatidylinositol, phosphatidylserine and sphingomyelin were the same in shed vesicles as in plasma membranes. In contrast, the molar proportions of cholesterol and diacylglycerol relative to sphingomyelin were almost twice those found in plasma membranes. The data demonstrate the existence of protein and lipid sorting mechanisms during the formation of shed vesicles when neutrophils are subject to sublytic complement attack. The term 'ectocytosis' is proposed to describe triggered shedding of right-side-out membrane vesicles from the surface of eukaryotic cells.
Modulation of the Lung Colonization of B16-F1 Melanoma Cells by Citrus Pectin (1992)

These findings imply that the galactose-containing carbohydrate side chains of CP might mimic or compete with the natural ligand(s) of the tumor galactoside-binding protein (gal-lectin) and thus affect cellular interactions relevant for metastasis.
Intraoperative Testosterone Assay for Virilizing Ovarian Tumor Topographic Assessment: Report of a Leydig Cell Tumor of the Ovary in a Premenopausal Woman with an Adrenal Incidentaloma (2002)

Ovarian virilizing tumors are rare and can lead to assessment difficulties because of their small size. A 41-yr-old female was referred for evaluation of hirsutism that had increased within the previous 3 yr. Menstrual cycle length was normal. Plasma testosterone was 3.9 ng/ml (normal range, 0.2-0.8 ng/ml), was not suppressible by 2 mg dexamethasone (4.3 ng/ml), and was increased (6.3 ng/ml) after three daily injections of hCG (5000 IU). Abdominal computed tomography scan showed an adrenal nodule (13 x 6 mm) that remained unchanged after 3 months. Ultrasound examination of the pelvis was normal. Ovarian and adrenal venous catheterization did not yield additional information. Topographic assessment was made by intraoperative measurement of testosterone in the samples taken from each ovarian vein (competitive chemiluminescent immunoassay ADVIA Centaur; right ovarian vein, 105 ng/ml; left ovarian vein, 5 ng/ml; peripheral blood, 7 ng/ml). Right annexectomy resulted in normalization of testosterone levels (0.22 ng/ml). Histopathological examination found a Leydig cell tumor of hilar type (1.5 cm). This observation illustrates the usefulness of intraoperative measurement of testosterone by a rapid automated technique for topographic assessment of ovarian virilizing tumor in premenopausal women.
AAL-2-A new ATM adaptation layer for small packet encapsulation and multiplexing (2002)

Asynchronous transfer mode (ATM) networks carry fixed-size cells within the network irrespective of the applications being supported. At the network edge or at the end equipment, an ATM adaptation layer (AAL) maps the services offered by the ATM network to the services required by the application. Many trunking applications that have voice compression and silence suppression require transmission of small delay-sensitive packets. Existing AALs are very inefficient for this purpose. In this paper, we discuss a new AAL called the AAL Type 2 (AAL-2), which allows very high efficiency for carrying small packets. We describe the basic principles and compare several alternatives with respect to transmission error performance, bandwidth efficiency, and delay/jitter performance. The results show that the AAL-2 adds significant value to packet telephony applications over ATM networks. We discuss the desirability of additional rebundling in the network and the need for a signaling protocol to communicate changes in native connections (voice calls) within the same ATM connection. We also describe how the principles of the AAL-2 are being used to define multiplexing protocols over the Internet and frame-relay networks.
Manipulation of Surface Properties by Patterning of Covalently Bound Polymer Brushes (2000)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTManipulation of Surface Properties by Patterning of Covalently Bound Polymer BrushesMarc Husemann, Michael Morrison, Didier Benoit, Jane Frommer, C. Mathew Mate, William D. Hinsberg, James L. Hedrick, and Craig J. HawkerView Author Information Center for Polymeric Interfaces and Macromolecular Assemblies, IBM Almaden Research Center 650 Harry Road, San Jose, California 95120-6099 Cite this: J. Am. Chem. Soc. 2000, 122, 8, 1844–1845Publication Date (Web):February 12, 2000Publication History Received3 May 1999Published online12 February 2000Published inissue 1 March 2000https://doi.org/10.1021/ja991450yCopyright © 2000 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views1834Altmetric-Citations188LEARN 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 InReddit Read OnlinePDF (143 KB) Get e-AlertsSUBJECTS:Organic compounds,Polymer brushes,Polymer films,Surface interactions,Thin films Get e-Alerts
Self-Referencing, Spectrally, or Spatially Encoded Spectral Interferometry for the Complete Characterization of Attosecond Electromagnetic Pulses (2005)

We propose a method for the complete characterization of attosecond duration electromagnetic pulses produced by high harmonic generation in an atomic gas. Our method is based on self-referencing spectral interferometry of two spectrally sheared extreme ultraviolet pulses, which is achieved by pumping the harmonic source with two sheared optical driving pulses. The resulting interferogram contains sufficient information to completely reconstruct the temporal behavior of the electric field. We demonstrate that such a method is feasible, and outline two possible experimental configurations.
Beyond Atopy: Multiple Patterns of Sensitization in Relation to Asthma in a Birth Cohort Study (2010)

IgE antibody responses do not reflect a single phenotype of atopy, but several different atopic vulnerabilities which differ in their relation with asthma presence and severity.
Syndecan-2 Is a Novel Target of Insulin-Like Growth Factor Binding Protein-3 and Is Over-Expressed in Fibrosis (2012)

Extracellular matrix deposition and tissue scarring characterize the process of fibrosis. Transforming growth factor beta (TGFβ) and Insulin-like growth factor binding protein-3 (IGFBP-3) have been implicated in the pathogenesis of fibrosis in various tissues by inducing mesenchymal cell proliferation and extracellular matrix deposition. We identified Syndecan-2 (SDC2) as a gene induced by TGFβ in an IGFBP-3-dependent manner. TGFβ induction of SDC2 mRNA and protein required IGFBP-3. IGFBP-3 independently induced production of SDC2 in primary fibroblasts. Using an ex-vivo model of human skin in organ culture expressing IGFBP-3, we demonstrate that IGFBP-3 induces SDC2 ex vivo in human tissue. We also identified Mitogen-activated protein kinase-interacting kinase (Mknk2) as a gene induced by IGFBP-3. IGFBP-3 triggered Mknk2 phosphorylation resulting in its activation. Mknk2 independently induced SDC2 in human skin. Since IGFBP-3 is over-expressed in fibrotic tissues, we examined SDC2 levels in skin and lung tissues of patients with systemic sclerosis (SSc) and lung tissues of patients with idiopathic pulmonary fibrosis (IPF). SDC2 levels were increased in fibrotic dermal and lung tissues of patients with SSc and in lung tissues of patients with IPF. This is the first report describing elevated levels of SDC2 in fibrosis. Increased SDC2 expression is due, at least in part, to the activity of two pro-fibrotic factors, TGFβ and IGFBP-3.
Short-term arginine deprivation results in large-scale modulation of hepatic gene expression in both normal and tumor cells: microarray bioinformatic analysis (2006)

Arginine-sensitive regulation appears to be an important homeostatic mechanism to coordinate cell response and nutrient availability in hepatic cells. Genes predicted as arginine-responsive in stringent microarray data analysis were confirmed by Northern blot and RT-PCR. Although the profile of arginine-responsive genes is altered and increased, a considerable portion of the "arginome" is maintained upon neoplastic transformation.
Diagnostic and Therapeutic Colonoscopy (1979)

The results of 662 therapeutic and diagnostic colonoscopic examinations were reviewed to assess the morbidity, clinical benefit, diagnostic accuracy, and indications for the procedure, with special emphasis on detection and endoscopic excision of small, occult, invasive cancers. Overall, the frequency of detecting occult lesions (19%), the (89%) ability to clarify questionable radiographic findings, and a substantial reduction in laparotomy-colotomy procedures required for removal of colonic polyps (88%), coupled with a low morbidity (3%) and low false-negative examination rate (1%) established colonoscopy as one of the most important advances in the management of colon disease in recent years. Although early experience suggests that small, occult, invasive carcinomas, when properly selected, could be adequately treated by endoscopic excision, larger series and longer follow-up periods are necessary to validate any conclusions regarding the decision to manage these lesions conservatively.
Oxyntomodulin Inhibits Food Intake in the Rat (2001)

Oxyntomodulin is derived from proglucagon processing in the intestine and the central nervous system. To date, no role in the central nervous system has been demonstrated. We report here that oxyntomodulin inhibits refeeding when injected intracerebroventricularly and into the hypothalamic paraventricular nucleus of 24-h fasted rats [intracerebroventricularly and into the paraventricular nucleus, 1 h, oxyntomodulin (1 nmol), 3.1 +/- 0.5 g; saline, 6.2 +/- 0.4 g; P < 0.005]. In addition, oxyntomodulin inhibits food intake in nonfasted rats injected at the onset of the dark phase (intracerebroventricularly, 1 h: oxyntomodulin, 3 nmol, 1.1 +/- 0.19 g vs. saline, 2.3 +/- 0.2 g; P < 0.05). This effect of oxyntomodulin on feeding is of a similar time course and magnitude as that of an equimolar dose of glucagon-like peptide-1. Other proglucagon-derived products investigated [glucagon, glicentin (intracerebroventricularly, 3 nmol; into the paraventricular nucleus, 1 nmol), and spacer peptide-1 (intracerebroventricularly and into the paraventricular nucleus, 3 nmol)] had no effect on feeding at any time point examined. The anorectic effect of oxyntomodulin (intracerebroventricularly, 3 nmol; into the paraventricular nucleus, 1 nmol) was blocked when it was coadministered with the glucagon-like peptide-1 receptor antagonist, exendin-(9-39) (intracerebroventricularly, 100 nmol; into the paraventricular nucleus, 10 nmol). However, oxyntomodulin has a lower affinity for the glucagon-like peptide-1 receptor compared with glucagon-like peptide-1 (IC(50): oxyntomodulin, 8.2 nM; glucagon-like peptide-1, 0.16 nM). One explanation for this is that there might be an oxyntomodulin receptor to which exendin-(9-39) can also bind and act as an antagonist.
Luminescence of n-i-p-i heterostructures (1986)

The luminescence properties of a new superlattice structure, called a n-i-p-i heterostructure, are described. The samples consist of GaAs quantum wells placed between alternately doped ${\mathrm{Al}}_{1\mathrm{\ensuremath{-}}\mathrm{x}}$${\mathrm{Ga}}_{\mathrm{x}}$As layers. The luminescence transitions between the quantized GaAs subbands are greatly influenced by the excitation-intensity-dependent electrostatic potential. The lowest subband luminescence transition agrees well with predictions for the ideal structure. In addition, distinct luminescence transitions from higher subbands are observed.
PAP: Detection of ultra rare mutations depends on P* oligonucleotides: ?Sleeping Beauties? awakened by the kiss of pyrophosphorolysis (2004)

Pyrophosphorolysis-activated polymerization (PAP) was initially developed to enhance the specificity of allele-specific PCR for detection of known mutations in the presence of a great excess of wild-type allele. The high specificity of PAP derives from the serial coupling of activation of a 3' blocked pyrophosphorolysis-activable oligonucleotide (P(*)) with extension of the unblocked, activated P(*). In theory, PAP can detect a copy of a single base mutation present in 3x10(11) copies of the wild-type allele. In practice, the selectivity of detection is limited by polymerase extension errors, a bypass reaction, from the unblocked oligonucleotide annealed to the opposing strand. Bi-directional PAP allele-specific amplification (Bi-PAP-A) is a derivative of PAP that uses two opposing pyrophosphorolysis activable oligonucleotides (P(*)) with one nucleotide overlap at their 3' termini. This eliminates the problematic bypass reaction. The selectivity of Bi-PAP-A was examined using lambda phage DNA as a model system. Bi-PAP-A selectively detected two copies of a rare mutated allele in the presence of at least 2x10(9) copies of the wild-type lambda phage DNA. We then applied Bi-PAP-A to direct detection of spontaneous somatic mutations in the lacI transgene in BigBlue transgenic mice at a frequency as low as 3x10(-9). A 370-fold variation in the frequency of a specific somatic mutation among different mouse samples was found, implying hyper-Poisson variance and clonal expansion of mutation occurring during early development. Bi-PAP-A is a simple, rapid, and general method capable of automation and particularly suited to detection of ultra rare mutations. We also show that P(*) oligonucleotides have the novel and unexpected property of high specificity to mismatches with the template throughout lengths of the P(*). Thus, PAP also can form the basis of microarray-based scanning or resequencing methods to detect virtually all mutations.