gebhart/patrepeval huggingface dataset:
Enzymatic Measurement of Sphingosine 1-Phosphate (1999)

Sphingosine 1-phosphate (SPP) is a sphingolipid metabolite which has novel dual actions acting as both an intracellular second messenger and a ligand for a family of G protein-coupled receptors. This paper describes a rapid enzymatic method to quantify mass levels of SPP in serum, mammalian tissues, and cultured cells. The assay utilizes an alkaline lipid extraction to selectively separate SPP from other phospholipids and sphingolipids, including sphingosine. Extracted SPP is efficiently converted to sphingosine by alkaline phosphatase treatment. Sphingosine thus formed is then quantitatively phosphorylated to [(32)P]SPP using recombinant sphingosine kinase and [gamma-(32)P]ATP. With this procedure we were able to obtain reproducible measurements of SPP over a broad range from 0.25 pmol to 2.5 nmol. In various rat tissues, levels of SPP varied between 0. 5 and 6 pmol/mg wet wt. The lowest levels were found in heart and testes, while brain contained the highest levels. The method was adapted easily to measure minute amounts of SPP present in various cultured cell types. The amount of SPP in cell extracts was proportional to the cell number and varied between 0.04 and 2 pmol/10(6) cells. Concurrent measurements of sphingosine levels revealed that its concentration was significantly higher than SPP in most cells and tissues. Furthermore, with this assay we were able to measure increases in intracellular SPP levels in rat pheochromocytoma PC12 cells after treatment with exogenous sphingosine or with nerve growth factor which stimulates sphingosine kinase activity.
Quantum gates with hot trapped ions (2002)

Summary form only given.In several applications of quantum communication and computation, one has to be able to perform some operations between two-level systems (qubits). For example, any quantum algorithm involves quantum gates between several qubits; in teleportation, one has to perform joint measurements between two qubits; in order to purify states, one also needs these operations. We previously proposed a way to implement these operations for a set of ions confined in a trap at zero temperature. It was based in the selective excitation of the center of mass mode of the collective motion using laser light, such that only when two atoms are in a given state, this state changes. In this contribution, we propose a different scheme to perform quantum gates between two ions in a trap. The most remarkable difference from our previous proposal is that the present one does not need to have the ions cooled to the ground state of the motional potential. It also operates in a time scale comparable to the oscillation frequency of the trap. On the other hand, it cannot be easily scaled up to include the presence of many ions, and therefore it does not represent an implementation of a quantum computer. The scheme is based on the interaction of the ions with laser fields, so that depending on the internal state of one ion, the other ion suffers a displacement in opposite directions. A laser with a space-dependent profile induces then a different rotation in the second ion, depending on its position. We study the conditions under which one can obtain optimal results, as well as the sensitivity to imperfections.
MYCNOS functions as an antisense RNA regulating MYCN (2015)

Amplification or overexpression of neuronal MYC (MYCN) is associated with poor prognosis of human neuroblastoma. Three isoforms of the MYCN protein have been described as well as a protein encoded by an antisense transcript (MYCNOS) that originates from the opposite strand at the MYCN locus. Recent findings suggest that some antisense long non-coding RNAs (lncRNAs) can play a role in epigenetically regulating gene expression. Here we report that MYCNOS transcripts function as a modulator of the MYCN locus, affecting MYCN promoter usage and recruiting various proteins, including the Ras GTPase-activating protein-binding protein G3BP1, to the upstream MYCN promoter. Overexpression of MYCNOS results in a reduction of upstream MYCN promoter usage and increased MYCN expression, suggesting that the protein-coding MYCNOS also functions as a regulator of MYCN ultimately controlling MYCN transcriptional variants. The observations presented here demonstrate that protein-coding transcripts can regulate gene transcription and can tether regulatory proteins to target loci.
CD34−Hematopoietic Stem Cells: Current Concepts and Controversies (2003)

Recent data have suggested that human CD34(-) hematopoietic stem cells (HSCs) exist, challenging the concept that HSCs necessarily and exclusively express the CD34 antigen. In mice, quiescent HSCs have been shown to be mostly CD34(-), but as a consequence of 5-fluorouracil treatment or cytokine stimulation, differentiate into CD34(+) cells. Of particular interest is a novel, specific marker to identify HSCs, namely the Hoechst dye efflux property, with which a distinct side population (SP) is identified. These SP cells are mostly CD34(-), highly enriched for long-term repopulating cells, and durably engraft in sublethally irradiated non-obese diabetic/severe combined immunodeficient mice. Using a semiquantitative reverse transcription-polymerase chain reaction, one of the ATP-binding cassette (ABC) transporters, the breast cancer resistance protein (Bcrp) or ABC transporter G2 (ABCG2), was found to be highly expressed in SP cells as well as other primitive HSCs and to sharply drop with hematopoietic differentiation. Enforced expression of the ABCG2 cDNA resulted in a robust SP phenotype and a reduction in hematopoietic maturation. These data suggest that the Bcrp/ABCG2 gene contributes importantly to the generation of the SP phenotype, which allows for the selection of immature, pluripotent HSCs. The isolation of Bcrp/ABCG2(+) cells appears to be an attractive tool to analyze and characterize HSCs, and may eventually allow for the purification of these cells for clinical purposes. In this review, current concepts on murine and human CD34(-) HSCs and their relationship with CD34(+) HSCs are discussed.
Disulfide bonding patterns and protein topologies (1993)

This paper examines the topological properties of protein disulfide bonding patterns. First, a description of these patterns in terms of partially directed graphs is developed. The topologically distinct disulfide bonding patterns available to a polypeptide chain containing n disulfide bonds are enumerated, and their symmetry and reducibility properties are examined. The theoretical probabilities are calculated that a randomly chosen pattern of n bonds will have any combination of symmetry and reducibility properties, given that all patterns have equal probability of being chosen. Next, the National Biomedical Research Foundation protein sequence and Brookhaven National Laboratories protein structure (PDB) databases are examined, and the occurrences of disulfide bonding patterns in them are determined. The frequencies of symmetric and/or reducible patterns are found to exceed theoretical predictions based on equiprobable pattern selection. Kauzmann's model, in which disulfide bonds form during random encounters as the chain assumes random coil conformations, finds that bonds are more likely to form with near neighbor cysteines than with remote cysteines. The observed frequencies of occurrence of disulfide patterns are found here to be virtually uncorrelated with the predictions of this alternative random bonding model. These results strongly suggest that disulfide bond pattern formation is not the result of random factors, but instead is a directed process. Finally, the PDB structure database is examined to determine the extrinsic topologies of polypeptides containing disulfide bonds. A complete survey of all structures in the database found no instances in which two loops formed by disulfide bonds within the same polypeptide chain are topologically linked. Similarly, no instances are found in which two loops present on different polypeptide chains in a structure are catenated. Further, no examples of topologically knotted loops occur. In contrast, pseudolinking has been found to be a relatively frequent event. These results show a complete avoidance of nontrivial topological entanglements that is unlikely to be the result of chance events. A hypothesis is presented to account for some of these observations.
Super-resolution imaging and detection of fluorescence from single molecules by scanning near-field optical microscopy (1995)

Scanning near-field microscopy (SNOM or NSOM) is a versatile and attractive scanning probe technique for imaging with subdiffraction-limited spatial resolution using visible light. At least three different types of images can be recorded simultaneously of the selected sample area, such as the topography, the near-field optical transmission, and the fluorescence from excited chromophores. We have built such a microscope, especially designed for achieving the high resolution and the sensitivity needed for single molecule detection. We report on optical near-field investigations of surface structures and thin polymer films that are doped with fluorescent dye molecules. The effective aperture diameters of the fiber tips used in the SNOM experiments were determined by a photon-scanning tunneling microscope (PSTM) giving values between 70 and 160 nm. The transmission imaging of transparent polymer phase gratings reveals the existence of different contrast mechanisms, which are either based on the inherent distance dependence of the optical near field or on the periodic change of boundary conditions for the electric field component of the light between the aperture and the sample. Furthermore, we demonstrate selective irreversible photobleaching of dye molecules at moderate concentration (10<sup>-5</sup> M) induced locally by the subwavelength-sized probe tip. Finally, we present fluorescence images showing single molecule detection in a thin solid film. The chromophores (rhodamine 6G) were embedded at low concentration (10<sup>-7</sup> M) in a 25-nm thin polyvinylbutyral film. A lateral resolution of 160 nm was achieved. We find that the signal strengths of the brightest fluorescent features vary considerably in a sequence of images (a typical single-molecule behavior), whereas the fluorescence background exhibits the usual photobleaching behavior of a large ensemble.
Inadequacy of high K+/nigericin for calibrating BCECF. I. Estimating steady-state intracellular pH (1996)

Intracellular pH (pHi) was measured in single vascular smooth muscle (VSM) cells, cultured from rabbit abdominal aorta, using 2',7'-bis(carboxyethyl)-5(6)-carboxyfluorescein (BCECF) on a microscope-based fluorescence system. Three lines of evidence are presented that using nigericin along with high external K+ to calibrate intracellular BCECF produces systematic errors in pHi. 1) The intrinsic buffering power (beta int), measured using weak bases (e.g., ammonium), was 2.5 times smaller than that measured using weak acids (e.g., propionic acid). This discrepancy became small if pHi had really been approximately 0.2 lower than what was estimated using nigericin-calibrated pHi values. 2) Total cellular buffering power (beta tot) in the presence of CO2/HCO-3 was measured and found to be much smaller than could account for the beta int, together with the contribution of CO2/HCO3 (beta CO2: assumed to be an open system buffer). If the true pHi values were approximately 0.2-0.4 lower than our nigericin-calibrated values, then the sum of beta int and beta CO2 equals beta tot. 3) A null technique was utilized for bracketing steady-state pHi; estimates of steady-state pHi using this null technique were approximately 0.2 lower than the high K+/nigericin-calibrated estimates. Four other cell types were examined: rat hepatocytes, rat corticotrophs, human keratinocytes, and rabbit fibroblasts. These other cells also displayed discrepancies between null and nigericin estimates of steady-state pHi, as well as differences between buffering power assessed using weak bases and acids. Finally, one potential source for these discrepancies is described: selecting an inappropriate external K+ to use with nigericin can produce systematic errors in pHi of approximately 0.1.
Protein Data Bank (PDB): Database of Three-Dimensional Structural Information of Biological Macromolecules (1998)

The Protein Data Bank (PDB) at Brookhaven National Laboratory, is a database containing experimentally determined three-dimensional structures of proteins, nucleic acids and other biological macromolecules, with approximately 8000 entries. Data are easily submitted via PDB's WWW-based tool AutoDep, in either mmCIF or PDB format, and are most conveniently examined via PDB's WWW-based tool 3DB Browser.
Ego-Splitting Framework (2017)

We propose ego-splitting, a new framework for detecting clusters in complex networks which leverage the local structures known as ego-nets (i.e. the subgraph induced by the neighborhood of each node) to de-couple overlapping clusters. Ego-splitting is a highly scalable and flexible framework, with provable theoretical guarantees, that reduces the complex overlapping clustering problem to a simpler and more amenable non-overlapping (partitioning) problem. We can scale community detection to graphs with tens of billions of edges and outperform previous solutions based on ego-nets analysis.
CHIR-124, a Novel Potent Inhibitor of Chk1, Potentiates the Cytotoxicity of Topoisomerase I Poisons In vitro and In vivo (2007)

CHIR-124 is a novel and potent Chk1 inhibitor with promising antitumor activities when used in combination with topoisomerase I poisons.
Dual-band transformer resonator oscillator with common-mode gain control (2010)

A new dual-mode oscillation scheme that adopts a transformer resonator is proposed. Switch-controlled common- and differential-mode operations enable the proposed oscillator to generate low and high frequency band, respectively. Simulated results for the proposed oscillator designed in CMOS 0.13 µmm process show dual-band frequencies of 2–2.87 and 5.75–9.36 GHz at the mode switch-on and switch-off, respectively, while dissipating 2.5 mA at 1.2 V supply.
Intestinal absorption of peptide enteral formulas in hypoproteinemic (volume expanded) rats (1989)

Previous studies have confirmed the improved tolerance of a peptide enteral compared to standard enteral alimentation in hypoalbuminemic, critically ill patients. Animal studies, including hypoproteinemic, volume-expanded rats, demonstrated that the protein hydrolysate of a peptide enteral formula was responsible for the enhanced absorption. The purpose of this study was to determine whether the composition of small MW peptides (protein hydrolysate) in two commercially available peptide enteral formulas would affect the rate of intestinal absorption and albumin clearance in intact jejunal loops before and during hypoproteinemia induced by iv infusion of Tyrode's solution in Sprague-Dawley rats. Net transmucosal water movement was calculated using a volume recovery method; albumin clearance was calculated using iv radiolabeled albumin. We studied three groups of animals during luminal perfusion with either Tyrode's solution, diet A containing 21% peptides, or diet B containing 56% peptides. When compared to luminal perfusion with Tyrode's solution (control animals), both diets significantly enhanced net transmucosal water absorption before volume expansion (p less than .05). With the induction of hypoproteinemia, diet B continued to stimulate water absorption when compared to control animals (p less than .01). Luminal perfusion with diet A failed to attenuate net water secretion induced by hypoproteinemia. Capillary and mucosal albumin clearance was similar for all groups studied. These findings suggest the percentage of small MW peptides may affect the rate of intestinal absorption in patients with acute kwashiorkor-like hypoalbuminemia.
Introduction to electronic document management systems (1993)

From the Publisher:
Introduction to Electronic Document Management Systems is a key resource for management and technical staff of organizations considering a transformation from traditional micrographics-based document storage and retrieval to the new systems based on electronic document capture. It will also be useful to organizations considering improving productivity by replacing systems based on processing documents on paper with electronic document management systems.
Carbon Structures with Three-Dimensional Periodicity at Optical Wavelengths (1998)

Porous carbons that are three-dimensionally periodic on the scale of optical wavelengths were made by a synthesis route resembling the geological formation of natural opal. Porous silica opal crystals were sintered to form an intersphere interface through which the silica was removed after infiltration with carbon or a carbon precursor. The resulting porous carbons had different structures depending on synthesis conditions. Both diamond and glassy carbon inverse opals resulted from volume filling. Graphite inverse opals, comprising 40-angstrom-thick layers of graphite sheets tiled on spherical surfaces, were produced by surface templating. The carbon inverse opals provide examples of both dielectric and metallic optical photonic crystals. They strongly diffract light and may provide a route toward photonic band-gap materials.
Deoxycytidine kinase and thymidine kinase activities in rat brain. (1993)

Deoxycytidine (CdR) kinase (E.C. 2.7.1.74) acts as a salvage enzyme in DNA biosynthesis, but little is known about this important nucleoside kinase in the brain. We report that CdR kinase activity in the 100,000 x g cytosolic fraction of normal adult rat brain cortex was 0.89 +/- 0.04 nmol/hr/mg protein which is twice that of the liver enzyme. For brain CdR kinase the apparent Km for CdR, ATP and Mg++ were 0.22, 1.1 and 0.63 mM, respectively. When the cytosolic preparation was incubated at 37 degrees C, CdR kinase activity rapidly decreased (t1/2 = 15 min); CdR (400 microM) protected the enzyme. Addition of DFDC (0 to 100 microM) competitively inhibited brain CdR kinase activity with Ki = 17 microM. DFDC elevated the apparent Km for CdR of brain CdR kinase 3.5-fold, from 0.22 to 0.8 mM. DFDC did not inhibit brain TdR kinase. AZT, which competitively inhibited TdR kinase (Ki = 0.6 microM), did not affect brain CdR kinase activity. These results indicate that the cytosol of rat brain contains CdR kinase which is inhibited by the deoxycytidine analog, DFDC. The enzyme is protected from thermal denaturation by CdR but not by TdR.
Merging microarray data from separate breast cancer studies provides a robust prognostic test (2008)

Rank-based features provide a stable way to integrate patient data from separate microarray studies due to invariance to data normalization, and such features can be combined into a useful predictor of distant metastases in breast cancer within a statistical modeling framework which begins to capture gene-gene interactions. Upon further confirmation on large-scale independent data, such prognostic signatures and tests could provide a powerful tool to guide adjuvant systemic treatment that could greatly reduce the cost of breast cancer treatment, both in terms of toxic side effects and health care expenditures.
TCR Signals Mediated by Src Family Kinases Are Essential for the Survival of Naive T Cells (2002)

The role of TCR signals triggered by recognition of self MHCs in maintaining the survival of naive peripheral T cells remains controversial. Here we examine the role of the Src family kinases, p56(lck) (Lck) and p59(fyn) (Fyn), in the survival of naive T cells. We show that long term survival requires a combination of signals transduced by Src family kinases and signals through the IL-7R. In the absence of either one, naive T cells die slowly, but if both signals are removed, cell loss is greatly accelerated. The TCR signal can be mediated by either Fyn or Lck at wild-type levels of expression, but not by Lck alone if expressed suboptimally. The disappearance of T cells in the absence of Fyn and Lck was associated with a complete loss of TCRzeta-chain phosphorylation and down-regulation of CD5, both of which are also MHC contact dependent, indicating that the Src family kinases are critical for transducing a TCR-MHC survival signal.
Holographic interferometer using single-mode optical fibers for the measurement of physical fields (1987)

A holographic interferometric method applied to the measurement of physical fields through the use of fibers is presented. In this method, a hologram, carrying the information of optical elements in the object beam, is made and set behind the output end of the optical fiber. This reconstructed object wave of the hologram is used as the measuring reference wave. When part of the fiber in the object beam is put into the measured physical field, the change of some parameter in the physical field should appear in the optical wave launching from the optical fiber, called the informational object wave. The interference field is formed behind the hologram by the informational object wave, and the measuring reference wave and parametric change of the physical field are revealed by the change in the interference field intensity.
Transforming growth factors and control of neoplastic cell growth (1987)

Transforming growth factors (TGFs) are peptides that affect the growth and phenotype of cultured cells and bring about in nonmalignant fibroblastic cells phenotypic properties that resemble those of malignant cells. Two types of TGFs have been well characterized. One of these, TGF alpha, is related to epidermal growth factor (EGF) and binds to the EGF receptor, whereas the other, TGF beta, is not structurally or functionally related to TGF alpha or EGF and mediates its effects via distinct receptors. TGF beta is produced by a variety of normal and malignant cells. Depending upon the assay system employed, TGF beta has both growth-inhibitory and growth-stimulating properties. Many of the mitogenic effects of TGF beta are probably an indirect result of the activation of certain growth factor genes in the target cell. The ubiquitous nature of the TGF beta receptor and the production of TGF beta in a latent form by most cultured cells suggests that the differing cellular responses to TGF beta are regulated either by events involved in the activation of the factor or by postreceptor mechanisms. The combined effects of TGF beta with other growth factors or inhibitors evidently play a central role in the control of normal and malignant cellular growth as well as in cell differentiation and morphogenesis. Since transforming growth factor as a concept has partially proven misleading and insufficient, there is a need to find a new nomenclature for these regulators of cellular growth and differentiation.
Homologous genes encode two distinct histidine-rich proteins in a cloned isolate of Plasmodium falciparum. (1986)

Two genes encoding distinct histidine-rich proteins in a Plasmodium falciparum clone exhibit high levels of homology, suggesting they have originated by duplication and divergence from a common ancestral sequence. Both genes have a similar interrupted structure and an exon that encodes closely related tandem repeats of very high histidine and alanine content. The most common repeat encoded by one gene, the hexapeptide Ala-His-His-Ala-Ala-Asp, differs in the sixth position from the most common repeat encoded by the other gene, the hexapeptide Ala-His-His-Ala-Ala-Asn. The divergence of the repeat domains is greater than that of the flanking regions, which exhibit 85-90% homology, including untranslated sequences. This suggests the tandem repeats are relatively labile elements within the genome that may provide the parasite with a means of rapid evolutionary change.