gebhart/patrepeval huggingface dataset:
Comparison of Reverse Transcriptases in Gene Expression Analysis (2004)

In most measurements of gene expression, mRNA is first reverse-transcribed into cDNA. The reverse transcription reaction is not very well understood, and it is expected to be the uncertain step in gene expression analysis. It can introduce errors produced by effects of mRNA secondary and tertiary structures, variation in priming efficiency, and properties of the reverse transcriptase (1)(2)(3)(4)(5). The aim of this work was to study the yield, reproducibility, and sensitivity of some commercially available reverse transcriptases on low to intermediate expressed genes by use of quantitative real-time PCR (QPCR).

Total RNA extraction, reverse transcription, and QPCR were performed as described in the Data Supplement that accompanies the online version of this Technical Brief at http://www.clinchem.org/content/vol50/issue9/ (6)(7). All reverse transcription reactions were run in replicates of four, using starting material from the same RNA pool prepared from bovine spleen, liver, or jejunum, which eliminated sample-to-sample variation (8). Only results for RNA from spleen are shown. Liver and jejunum gave similar results, which are provided in the online Data Supplement. To determine absolute reverse transcription yields, we added an artificial RNA MultiStandard (Roboscreen) to samples (9)(10). Eight reverse transcriptases were studied: Moloney murine leukemia virus RNase H− (MMLVH; Promega); MMLV (Promega); avian myeloblastosis virus (AMV; Promega); Improm-II (Promega); Omniscript (Qiagen); cloned AMV (cAMV; Invitrogen); ThermoScript RNase H− (Invitrogen); and SuperScript III RNase H− …
Immunoassay of low concentrations of albumin in urine by latex particle counting. (1988)

We describe here a nonisotopic immunoassay, based on particle-counting technology, for the determination of urinary albumin. The assay takes only 35 min and has been fully automated on the IMPACT (Acade Diagnostic Systems, Brussels, Belgium) machine. The system measures albumin within a linear range between 6.25 and 50 mg/L and has a detection limit of 0.4 mg/L. Analytical recoveries at three concentrations ranged between 96% and 102%. Within-run precision ranged from 1.6% to 9.5%. The method was compared with a commercial nephelometric immunoassay system and a correlation coefficient of 0.996 was found for 216 urine samples. No antigen excess affects the shape of the curve in our system, whereas in nephelometry a 3 g/L solution of albumin starts to decrease the dose-response curve.
OX40 Costimulation Enhances Interleukin-4 (IL-4) Expression at Priming and Promotes the Differentiation of Naive Human CD4+ T Cells Into High IL-4–Producing Effectors (1998)

Th2 cell development is critically dependent on the presence of interleukin-4 (IL-4) at priming. The cellular origin and the mechanisms regulating this early production of IL-4 at the site of naive T-cell priming are extensively investigated. We previously reported that anti-CD3-activated and CD28-costimulated naive human CD4(+) T cells themselves release very low but sufficient levels of IL-4 to support their development into high IL-4-producing cells. We show here that ligation of OX40 Ag, a member of the tumor necrosis factor receptor (TNF-R) family, on activated umbilical cord blood CD4(+) T cells upregulates IL-4 production at priming and thereby promotes their development into effector cells producing high levels of the type 2 cytokines IL-4, IL-5, and IL-13. OX40 ligation increases four times the expression of IL-4 mRNA after 48 hours of anti-CD3/B7.1 activation and significantly augments the release of IL-4 and IL-13 in primary cultures. The effects of OX40 costimulation on Th cell differentiation are observed in the presence of optimal and suboptimal CD28 stimulation. Because OX40 ligand is expressed on dendritic cells, the OX40 costimulation pathway may be involved in the physiological regulation of Th cell development by augmenting the differentiation of IL-4-producing cells.
Detection of macrophage activity in atherosclerosis in vivo using multichannel, high-resolution laser scanning fluorescence microscopy (2006)

Molecular and cellular mechanisms of atherogenesis and its treatment are largely being unraveled by in vitro techniques. We describe methodology to directly image macrophage cell activity in vivo in a murine model of atherosclerosis using laser scanning fluorescence microscopy (LSFM) and a macrophage-targeted, near-infrared fluorescent (NIRF) magnetofluorescent nanoparticle (MFNP). Atherosclerotic apolipoprotein E deficient (apoE -/-) mice (n=10) are injected with MFNP or 0.9% saline, and wild-type mice (n=4) are injected with MFNP as additional controls. After 24 h, common carotid arteries are surgically exposed and prepared for LSFM. Multichannel LSFM of MFNP-enhanced carotid atheroma (5x5-microm in-plane resolution) shows a strong focal NIRF signal, with a plaque target-to-background ratio of 3.9+/-1.8. Minimal NIRF signal is observed in control mice. Spectrally resolved indocyanine green (ICG) fluorescence angiograms confirm the intravascular location of atheroma. On ex vivo fluorescence reflectance imaging, greater NIRF plaque signal is seen in apoE -/- MFNP mice compared to controls (p<0.01). The NIRF signal correlates well with immunostained macrophages, both by stained surface area (r=0.77) and macrophage number (r=0.86). The validated experimental methodology thus establishes a platform for investigating macrophage activity in atherosclerosis in vivo, and has implications for the detection of clinical vulnerable plaques.
The growth factor requirements of STRO-1-positive human bone marrow stromal precursors under serum-deprived conditions in vitro (1995)

Factors that regulate the growth and development of primitive bone marrow stromal cell precursors are not well defined. We have examined 25 purified recombinant growth factors for their ability to initiate and support clonogenic growth of fibroblast colony-forming cells (CFU-F) from adult human bone marrow. Assays were performed using bone marrow mononuclear cells (BMMNC) enriched in CFU-F by magnetic-activated cell sorting (MACS) using the monoclonal antibody (MoAb) STRO-1. A serum-deprived assay was developed to avoid components of fetal calf serum (FCS) that may mask or otherwise modify the response of CFU-F to exogenously added factors. L-ascorbate and the glucocorticoid dexamethasone were found to be essential for CFU-F colony development under serum-deprived conditions. Importantly, clonogenic growth of CFU-F in this culture system was absolutely dependent on an exogenous source of growth factor. Platelet-derived growth factor-BB (PDGF) and epidermal growth factor (EGF) demonstrated the greatest ability to support colony growth. Colony formation was dose-dependent, with half-maximal colony numbers at approximately 0.2 ng/mL for either factor and plateau numbers at concentrations in excess of 1.0 ng/mL. Simultaneous addition of PDGF and EGF had no effect on the number of colonies initiated but resulted in dose-dependent increases in mean colony diameter that were significant (P < or = .05) when compared with the effect of either factor alone or with the size of colonies elicited in control cultures by 20% FCS. Fluorescence-activated cell sorting (FACS) of BMMNC using MoAbs to the alpha chain of the PDGF receptor and to the EGF receptor in combination with the Moab STRO-1 demonstrated constitutive expression of both receptors by greater than 90% on CFU-F. Receptors for insulin-like growth factor-1 (IGF-1) and nerve growth factor (NGF) were also detected on STRO-1+ CFU-F, but in vitro both IGF-1 and NGF did not support colony growth. This report demonstrates the development of a simple, reproducible, and stringent culture system for the growth and assay of stromal precursors under serum-deprived conditions and represents an important prerequisite for future studies of the role of growth factors in the regulation of stromal cell proliferation, differentiation, and development.
The vessel wall reaction in restenosis. (1997)

Coronary angioplasty imposes injury on the coronary artery during the procedure to achieve adequate revascularization. The arterial response to that injury is critical to both the acute and long-term success or failure of the procedure. As newer technologies become clinically available, it is increasingly evident that a final common response to angioplasty is neointimal formation, and adventitial contraction known as remodelling. Both procedures appear to occur to varying degrees, and similarly appear dependent on the degree of injury. Neointimal hyperplasia is a major factor in the restenosis problem, although others are clearly important. Additional factors include thrombus, intimal and medial dissections and elastic recoil of the arterial wall. The proportion of the restenosis problem caused by each is unclear, but current efforts to solve restenosis centre on limiting neointimal hyperplasia, the primary response to injury of the vessel. This paper will review arterial injury during revascularization in both patients and animal models, with special emphasis of the nature and formation of neointimal hyperplasia.
Glycosaminoglycans of human dental pulp. (1976)

Dental pulps were obtained from sound human permanent molars and premolars. The pulps were treated to remove lipid, protein and nucleic acid and glycosaminoglycans were finally isolated by ethanol precipitation. Electrophoretic examination and CPC-cellulose profiles revealed the presence of hyaluronic acid, dermatan sulphate, chondroitin 4 sulphate and chondroitin 6 sulphate. Hyaluronic acid accounted for only a low percentage of the total glycosaminoglycan content while dermatan sulphate was present in unusually high amounts. Chondroitin 4 and 6 sulphates represented the major glycosaminoglycan fraction.
Detection of Aminium Ion Intermediates:  N-Cyclopropyl versus N-Carboxymethyl Groups as Reporters (2001)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTDetection of Aminium Ion Intermediates: N-Cyclopropyl versus N-Carboxymethyl Groups as ReportersRheem A. Totah and Robert P. HanzlikView Author Information Department of Medicinal Chemistry University of Kansas Malott Hall 4048, 1251 Wescoe Hall Drive Lawrence, Kansas 66045-7582 Cite this: J. Am. Chem. Soc. 2001, 123, 41, 10107–10108Publication Date (Web):September 25, 2001Publication History Received9 July 2001Published online25 September 2001Published inissue 1 October 2001https://pubs.acs.org/doi/10.1021/ja011648uhttps://doi.org/10.1021/ja011648urapid-communicationACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views833Altmetric-Citations7LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Ions,Kinetics,Oxidation,Peptides and proteins,Ring opening reactions Get e-Alerts
Transformation of mammalian cells to antibiotic resistance with a bacterial gene under control of the SV40 early region promoter. (1982)

A bacterial gene (neo) conferring resistance to neomycin-kanamycin antibiotics has been inserted into SV40 hybrid plasmid vectors and introduced into cultured mammalian cells by DNA transfusion. Whereas normal cells are killed by the antibiotic G418, those that acquire and express neo continue to grow in the presence of G418. In the course of the selection, neo DNA becomes associated with high molecular weight cellular DNA and is retained even when cells are grown in the absence of G418 for extended periods. Since neo provides a marker for dominant selections, cell transformation to G418 resistance is an efficient means for cotransformation of nonselected genes.
Fibronectin and fibrin gel structure. (1985)

Plasma fibronectin is covalently incorporated into alpha-chains of fibrin gels in the presence of Factor XIII activated by thrombin (FXIIIaT) but not by Factor XIII activated by the snake venom enzyme batroxobin (FXIIIaB). FXIIIaB catalyzes introduction of gamma-gamma cross-links in fibrin but cross-linked alpha-chains are not formed. In the presence of FXIIIaT, fibrin gels formed by batroxobin incorporated fibronectin and the alpha-chains are cross-linked indicating that FXIIIaB has a different substrate specificity from FXIIIaT. In the presence of FXIIIaT the incorporation of fibronectin approaches 1 mol/340 kDa unit weight of fibrin. Fibronectin when present in a fibrinogen thrombin mixture containing FXIII does not influence the clotting time of the system nor the release of fibrinopeptides. Incorporation of fibronectin is not appreciable before the gel point. This indicates that the polymerization and gelation of fibrinogen is essentially not perturbed by the presence of fibronectin and that fibrin in the gel matrix rather than the fibrin polymers formed prior to gel point is the preferred structure for fibronectin incorporation. Incorporation of fibronectin into fibrin gels during formation leads to an increase in turbidity and a small decrease in Ks (permeability coefficient). This suggests that the width of the strands in the gel increases as a result of fibronectin incorporation. Fibronectin is also incorporated into preformed gels having completely cross-linked gamma- and alpha-chains perhaps indicating that the sites in fibrin involved in fibronectin incorporation are different from those involved in fibrin cross-linking. FXIIIaT appeared to be adsorbed to fibrin gel matrix in the presence but not in the absence of calcium ions.
Ketone Diester Ingestion Impairs Time-Trial Performance in Professional Cyclists (2017)

We investigated the effect of pre- "race" ingestion of a 1,3-butanediol acetoacetate diester on blood ketone concentration, substrate metabolism and performance of a cycling time trial (TT) in professional cyclists. In a randomized cross-over design, 10 elite male cyclists completed a ~31 km laboratory-based TT on a cycling ergometer programmed to simulate the 2017 World Road Cycling Championships course. Cyclists consumed a standardized meal [2 g/kg body mass (BM) carbohydrate (CHO)] the evening prior to a trial day and a CHO breakfast (2 g/kg BM CHO) with 200 mg caffeine on the morning of a trial day. Cyclists were randomized to consume either the ketone diester (2 × 250 mg/kg) or a placebo drink, followed immediately by 200 mL diet cola, given ~ 30 min before and immediately prior to commencing a 20 min incremental warm-up. Blood samples were collected prior to and during the warm-up, pre- and post- TT and at regular intervals after the TT. Urine samples were collected pre- and post- warm-up, immediately post TT and 60 min post TT. Pre-exercise ingestion of the diester resulted in a 2 ± 1% impairment in TT performance that was associated with gut discomfort and higher perception of effort. Serum β-hydroxybutyrate, serum acetoacetate, and urine ketone concentrations increased from rest following ketone ingestion and were higher than placebo throughout the trial. Ketone ingestion induces hyperketonemia in elite professional cyclists when in a carbohydrate fed state, and impairs performance of a cycling TT lasting ~50 min.
Compact broadband continuum source based onmicrochip laser pumped microstructured fibre (2001)

A 300 nm broadband visible continuum has been generated in a 1.8 m length of microstructured fibre pumped at 532 nm by 0.8 ns pulses from a frequency-doubled passively Q-switched Nd:YAG microchip laser. With nanosecond pulses, self-phase-modulation is negligible, and the continuum generation is dominated by the interplay of Raman and parametric effects.
Deep sequencing of RNA from immune cell-derived vesicles uncovers the selective incorporation of small non-coding RNA biotypes with potential regulatory functions (2012)

Cells release RNA-carrying vesicles and membrane-free RNA/protein complexes into the extracellular milieu. Horizontal vesicle-mediated transfer of such shuttle RNA between cells allows dissemination of genetically encoded messages, which may modify the function of target cells. Other studies used array analysis to establish the presence of microRNAs and mRNA in cell-derived vesicles from many sources. Here, we used an unbiased approach by deep sequencing of small RNA released by immune cells. We found a large variety of small non-coding RNA species representing pervasive transcripts or RNA cleavage products overlapping with protein coding regions, repeat sequences or structural RNAs. Many of these RNAs were enriched relative to cellular RNA, indicating that cells destine specific RNAs for extracellular release. Among the most abundant small RNAs in shuttle RNA were sequences derived from vault RNA, Y-RNA and specific tRNAs. Many of the highly abundant small non-coding transcripts in shuttle RNA are evolutionary well-conserved and have previously been associated to gene regulatory functions. These findings allude to a wider range of biological effects that could be mediated by shuttle RNA than previously expected. Moreover, the data present leads for unraveling how cells modify the function of other cells via transfer of specific non-coding RNA species.
A Kinematic Notation for Lower-Pair Mechanisms Based on Matrices (1955)

Abstract A symbolic notation devised by Reuleaux to describe mechanisms did not recognize the necessary number of variables needed for complete description. A reconsideration of the problem leads to a symbolic notation which permits the complete description of the kinematic properties of all lower-pair mechanisms by means of equations. The symbolic notation also yields a method for studying lower-pair mechanisms by means of matrix algebra; two examples of application to space mechanisms are given.
Transmitter Architecture for CA: Carrier Aggregation in LTE-Advanced Systems (2013)

CA has already found its place in the deployment of 4G wireless networks. It successfully shows its value as an efficient way to increase the signal bandwidth within the available spectrum. This article is focused on demonstrating and analyzing the possible transmitter architecture solutions for CA. Further, the benefits and issues of using concurrent dual-band transmitter architecture are investigated. The recent progress on deploying concurrent dual-band PAs has been surveyed, where recent published literatures reported significant improvement on the concurrent dual-band PA design and achievable efficiency. The challenges present in the development of the linearization schemes for concurrent dual-band transmitters are addressed and possible solutions are studied.
Interleukin 6 receptor antibody inhibits muscle atrophy and modulates proteolytic systems in interleukin 6 transgenic mice. (1996)

The muscles of IL-6 transgenic mice suffer from atrophy. Experiments were carried out on these transgenic mice to elucidate activation of proteolytic systems in the gastrocnemius muscles and blockage of this activation by treatment with the anti-mouse IL-6 receptor (mIL-6R) antibody. Muscle atrophy observed in 16-wk-old transgenic mice was completely blocked by treatment with the mIL-6R antibody. In association with muscle atrophy, enzymatic activities and mRNA levels of cathepsins (B and L) and mRNA levels of ubiquitins (poly- and mono-ubiquitins) increased, whereas the mRNA level of muscle-specific calpain (calpain 3) decreased. All these changes were completely eliminated by treatment with the mIL-6R antibody. This IL-6 receptor antibody could, therefore, be effective against muscle wasting in sepsis and cancer cachexia, where IL-6 plays an important role.
Interaction of calmodulin with myosin light chain kinase and cAMP-dependent protein kinase in bovine brain. (1981)

Myosin light chain kinase and a fraction of type II cAMP-dependent protein kinase have been partially purified from bovine brain by affinity chromatography on calmodulin-Sepharose. The myosin kinase was purified approximately 3700-fold and has an estimated molecular weight of 130,000 +/- 10,000 by sodium dodecyl sulfate gel electrophoresis. A fraction of soluble cAMP-dependent protein kinase also bound to calmodulin-Sepharose and was purified 2300-fold. A fraction of this cAMP-dependent protein kinase after purification by glycerol gradient centrifugation was shown to contain the two subunits of calcineurin, a major calmodulin-binding protein in brain, and the two subunits of type II cAMP-dependent protein kinase in a ratio of 1:1:2:2. Its sedimentation coefficient was 8.1 S and 9.0 S when centrifuged in the absence or presence of calmodulin, suggesting the formation of a complex between calmodulin and protein kinase. Our results suggest the possibility that calcineurin may be involved in the interaction between the protein kinase and calmodulin. Furthermore, our studies imply that the regulatory subunit of the cAMP-dependent protein kinase, but not the catalytic subunit, is the site of interaction with calmodulin since the catalytic subunit of protein kinase was partially resolved from the complex by cAMP.
Analysis of Polycyclic Aromatic Hydrocarbons Using Desorption Atmospheric Pressure Chemical Ionization Coupled to a Portable Mass Spectrometer (2014)

Desorption atmospheric pressure chemical ionization (DAPCI) is implemented on a portable mass spectrometer and applied to the direct detection of polycyclic aromatic hydrocarbons (PAHs) and alkyl substituted benzenes. The presence of these compounds in the environment poses a significant threat to the health of both humans and wildlife because of their carcinogenic, toxic, and mutagenic properties. As such, instant detection outside of the laboratory is of particular importance to allow in-situ measurement at the source. Using a rapid, high throughput, miniature, handheld mass spectrometer, several alkyl substituted benzenes and PAHs (i.e., 1,2,3,5-tetramethylbenzene, pentamethylbenzene, hexamethylbenzene, fluoranthene, anthracene, benzo[k]fluoranthene, dibenz[a,h]anthracene, acenaphthene, indeno[1,2,3-c,d]pyrene, 9-ethylfluorene, and 1-benzyl-3-methyl-naphthalene) were identified and characterized using tandem mass spectrometry (MS/MS) from ambient surfaces, in the open air. This method can provide almost instantaneous information while minimizing sample preparation, which is advantageous in terms of both cost and simplicity of analysis. This MS-based technique is applicable to a wide range of environmental organic molecules.