gebhart/patrepeval huggingface dataset:
Federated two‐dimensional electrophoresis database: A simple means of publishing two‐dimensional electrophoresis data (1996)

While a two-dimensional electrophoresis (2-DE) database is a relatively old concept, in recent years it generated renewed interest within the 2-DE community due to two main factors: (i) The high reproducibility of the current 2-DE method allows 2-DE images to be exchanged and compared between laboratories. (ii) The recent development of faster and more powerful techniques for protein identification such as microsequencing, matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS) and amino acid composition makes the production of reference protein maps and 2-DE databases cost- and time-effective. Additionally, the Internet network's current increase in popularity, combined with the rapid growth of Internet-connected laboratories, provides a straightforward means of publishing and sharing 2-DE data. While a small number of laboratories have already successfully published their data over the net, the increasing number of 2-DE database servers that are currently being set up will sooner or later require some kind of standardization. Unfortunately, standardization can be a long and cumbersome process inevitably leading to undesirable compromises. A federated database offers a simple and efficient way to publish and share 2-DE data without the need for standardization. Taking advantage of Internet protocols such as World Wide Web, they allow each laboratory to maintain their own database and to interconnect it with other similar databases through the use of active cross-references. This paper first presents guidelines for building a federated 2-DE database that may easily be followed by most laboratories. It then briefly reviews the state-of-the-art in networked 2-DE databases, and finally describes the SWISS-2DPAGE database which fully implements the concept of a federated 2-DE database.
The metal carbonyls. V. Physiological properties. VI. Derivatives (1938)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe metal carbonyls. V. Physiological properties. VI. DerivativesWilliam E. Trout Cite this: J. Chem. Educ. 1938, 15, 2, 77Publication Date (Print):February 1, 1938Publication History Received3 August 2009Published online1 February 1938Published inissue 1 February 1938https://doi.org/10.1021/ed015p77RIGHTS & PERMISSIONSArticle Views65Altmetric-Citations6LEARN 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 PDF (5 MB) Get e-Alerts Get e-Alerts
Coprescription of Tamoxifen and Medications That Inhibit CYP2D6 (2010)

Evidence has emerged that the clinical benefit of tamoxifen is related to the functional status of the hepatic metabolizing enzyme cytochrome P450 2D6 (CYP2D6). CYP2D6 is the key enzyme responsible for the generation of the potent tamoxifen metabolite, endoxifen. Multiple studies have examined the relationship of CYP2D6 status to breast cancer outcomes in tamoxifen-treated women; the majority of studies demonstrated that women with impaired CYP2D6 metabolism have lower endoxifen concentrations and a greater risk of breast cancer recurrence. As a result, practitioners must be aware that some of the most commonly prescribed medications coadministered with tamoxifen interfere with CYP2D6 function, thereby reducing endoxifen concentrations and potentially increasing the risk of breast cancer recurrence. After reviewing the published data regarding tamoxifen metabolism and the evidence relating CYP2D6 status to breast cancer outcomes in tamoxifen-treated patients, we are providing a guide for the use of medications that inhibit CYP2D6 in patients administered tamoxifen.
Plasmon Resonance Methods in GPCR Signaling and Other Membrane Events (2005)

The existence of surface guided electromagnetic waves has been theoretically predicted from Maxwell's equations and investigated during the first decades of the 20th century. However, it is only since the late 1960's that they have attracted the interest of surface physicists and earned the moniker of "surface plasmon". With the advent of commercially available instruments and well established theories, the technique has been used to study a wide variety of biochemical and biotechnological phenomena. Spectral response of the resonance condition serves as a sensitive indicator of the optical properties of thin films immobilized within a wavelength of the surface. This enhanced surface sensitivity has provided a boon to the surface sciences, and fosters collaboration between surface chemistry, physics and the ongoing biological and biotechnological revolution. Since then, techniques based on surface plasmons such as Surface Plasmon Resonance (SPR), SPR Imaging, Plasmon Waveguide Resonance (PWR) and others, have been increasingly used to determine the affinity and kinetics of a wide variety of real time molecular interactions such as protein-protein, lipid-protein and ligand-protein, without the need for a molecular tag or label. The physical-chemical methodologies used to immobilize membranes at the surface of these optical devices are reviewed, pointing out advantages and limitations of each method. The paper serves to summarize both historical and more recent developments of these technologies for investigating structure-function aspects of these molecular interactions, and regulation of specific events in signal transduction by G-protein coupled receptors (GPCRs).
Hydrocarbons of Blue-Green Algae: Geochemical Significance (1969)

The hydrocarbon compositions of 11 species of blue-green algae are simple and qualitatively similar. Three marine coccoids contain only monoenoic and dienoic C(19) hydrocarbons. Hydrocarbons of the remaining eight species are C(15) to C(18). Hydrocarbons of higher molecular weight (C(20) or more) were not detected. Blue-green algae do not appear to be the source material for the longchain (greater than 20 carbons) hydrocarbons found in ancient sediments.
Polymorphisms in leucine-rich repeat genes are associated with autism spectrum disorder susceptibility in populations of European ancestry (2010)

Overall, our findings implicate the neuronal leucine-rich genes LRRN3 and LRRTM3 in ASD susceptibility.
Dermatan sulphate-rich proteoglycan associates with rat tail-tendon collagen at the d band in the gap region (1981)

Rat tail tendon was stained with a cationic phthalocyanin dye, Cupromeronic Blue, in a 'critical-electrolyte-concentration' method [Scott (1980) Biochem. J. 187, 887-891] specifically to demonstrate proteoglycan by electron microscopy. Hyaluronidase digestion in the presence of proteinase inhibitors corroborated the results. Collagen was stained with uranyl acetate and/or phosphotungstic acid to demonstrate the banding pattern a-e in the D period. Proteoglycan was distributed about the collagen fibrils in an orthogonal array, the transverse elements of which were located almost exclusively at the d band, in the gap zone. The proteoglycan may inhibit (1) fibril radial growth by accretion of collagen molecules or fibril fusion, through interference with cross-linking, and (2) calcification by occupying the holes in the gap region later to be filled with hydroxyapatite.
Controlling Morphology in Polymer–Fullerene Mixtures (2007)

Methods to determine the agglomerated–amorphous ratio of P3HT in P3HT:PCBM solar cell mixtures, and control the degree of agglomeration–crystallinity of P3HT in the final device using a solvent mixing method and no further heat-treatment or preparation of the polymer are presented. As-cast devices have an efficiency of ∼4%.
Leveraging multiple query logs to improve language models for spoken query recognition (2009)

A voice search system requires a speech interface that can correctly recognize spoken queries uttered by users. The recognition performance strongly relies on a robust language model. In this work, we present the use of multiple data sources, with the focus on query logs, in improving ASR language models for a voice search application. Our contributions are three folds: (1) the use of text queries from web search and mobile search in language modeling; (2) the use of web click data to predict query forms from business listing forms; and (3) the use of voice query logs in creating a positive feedback loop. Experiments show that by leveraging these resources, we can achieve recognition performance comparable to, or even better than, that of a previously deploy system where a large amount of spoken query transcripts are used in language modeling.
Detection of human parvovirus B19 DNA PCR products by RNA probe hybridization enzyme immunoassay (1994)

We have developed an RNA probe hybridization enzyme immunoassay for detection of human parvovirus B19 PCR-amplified DNA. The assay is easy to perform and increases assay sensitivity without the added inconvenience and risk of false-positive results associated with nested PCR.
Infection of Glial Cells by the Human Polyomavirus JC Is Mediated by an N-Linked Glycoprotein Containing Terminal α(2-6)-Linked Sialic Acids (1998)

The human JC polyomavirus (JCV) is the etiologic agent of the fatal central nervous system (CNS) demyelinating disease progressive multifocal leukoencephalopathy (PML). PML typically occurs in immunosuppressed patients and is the direct result of JCV infection of oligodendrocytes. The initial event in infection of cells by JCV is attachment of the virus to receptors present on the surface of a susceptible cell. Our laboratory has been studying this critical event in the life cycle of JCV, and we have found that JCV binds to a limited number of cell surface receptors on human glial cells that are not shared by the related polyomavirus simian virus 40 (C. K. Liu, A. P. Hope, and W. J. Atwood, J. Neurovirol. 4:49-58, 1998). To further characterize specific JCV receptors on human glial cells, we tested specific neuraminidases, proteases, and phospholipases for the ability to inhibit JCV binding to and infection of glial cells. Several of the enzymes tested were capable of inhibiting virus binding to cells, but only neuraminidase was capable of inhibiting infection. The ability of neuraminidase to inhibit infection correlated with its ability to remove both alpha(2-3)- and alpha(2-6)-linked sialic acids from glial cells. A recombinant neuraminidase that specifically removes the alpha(2-3) linkage of sialic acid had no effect on virus binding or infection. A competition assay between virus and sialic acid-specific lectins that recognize either the alpha(2-3) or the alpha(2-6) linkage revealed that JCV preferentially interacts with alpha(2-6)-linked sialic acids on glial cells. Treatment of glial cells with tunicamycin, but not with benzyl N-acetyl-alpha-D-galactosaminide, inhibited infection by JCV, indicating that the sialylated JCV receptor is an N-linked glycoprotein. As sialic acid containing glycoproteins play a fundamental role in mediating many virus-cell and cell-cell recognition processes, it will be of interest to determine what role these receptors play in the pathogenesis of PML.
Delayed infusion of normal donor cells after MHC-matched bone marrow transplantation provides an antileukemia reaction without graft-versus-host disease. (1993)

When allogeneic BMT is used for the treatment of leukemia, depletion of T cells from the donor BM to avoid GVHD may be accompanied by persistence of host cells and post-transplant relapse. In this report, a murine model of MHC-compatible BMT was used to show that delayed infusion of immunocompetent donor cells early after T cell-deficient BMT eliminated residual host cells and provided an antileukemic effect without causing lethal GVHD. AKR (H-2k) recipient mice were pre-conditioned with 9 Gy total body irradiation (LD50) and transplanted with 10(7) BM cells from MHC-matched B10.BR donors. These mice did not develop GVHD and became stable, long-term mixed (donor-host) T cell chimeras. In this model, mixed or incomplete donor T cell chimerism was associated with decreased GVL reactivity. AKR hosts that were transplanted with B10.BR bone marrow admixed with 3 x 10(7) B10.BR spleen cells (as a source of T cells) became complete donor T cell chimeras, but they developed severe and lethal GVHD. However, when the infusion of donor spleen cells was delayed until 21 days after BMT, few mice exhibited any clinical signs of GVHD, and > 95% of the mice became long-term survivors. The infused spleen cells eliminated residual host T cells by 21 days after infusion, and most chimeras were able to resist a supralethal challenge with AKR leukemia/lymphoma cells. Thus, post-transplant adoptive immunotherapy with normal mononuclear cells from the marrow donor may be an effective way to eliminate residual disease or treat leukemia relapse after BMT without causing significant GVHD.
Positive contrast visualization of iron oxide‐labeled stem cells using inversion‐recovery with ON‐resonant water suppression (IRON) (2007)

In proton magnetic resonance imaging (MRI) metallic substances lead to magnetic field distortions that often result in signal voids in the adjacent anatomic structures. Thus, metallic objects and superparamagnetic iron oxide (SPIO)-labeled cells appear as hypointense artifacts that obscure the underlying anatomy. The ability to illuminate these structures with positive contrast would enhance noninvasive MR tracking of cellular therapeutics. Therefore, an MRI methodology that selectively highlights areas of metallic objects has been developed. Inversion-recovery with ON-resonant water suppression (IRON) employs inversion of the magnetization in conjunction with a spectrally-selective on-resonant saturation prepulse. If imaging is performed after these prepulses, positive signal is obtained from off-resonant protons in close proximity to the metallic objects. The first successful use of IRON to produce positive contrast in areas of metallic spheres and SPIO-labeled stem cells in vitro and in vivo is presented.
Secondary Structure Formation and LCST Behavior of Short Elastin-Like Peptides (2008)

This contribution investigates the effects of chain length and chemical composition on the secondary structure and LCST behavior of a library of short, elastin-like peptides based on the GVGVP motif. CD experiments revealed that most of the investigated peptides showed the typical elastin conformational behavior with a decrease in random coil and an increase in beta-turn character with increasing temperature. For several peptides, LCST behavior was observed in aqueous NaCl solutions containing 10 mg/mL peptide. By extrapolation of the LCSTs measured at different NaCl concentrations to zero-salt concentration, apparent LCSTs were determined. The apparent LCST was found to decrease with increasing peptide chain length, which correlated well with the trend in the predicted partition coefficients. The apparent LCST of the peptides could be manipulated by successive replacement of the valine residues by more hydrophobic isoleucine, leucine, or phenylalanine residues. Within a particular series of variants, the apparent LCST was found to decrease with an increasing number of valine replacements, which also correlated well with the predicted evolution of the partition coefficient. Although the relative importance of the overall peptide hydrophobicity and the conformational preferences of the constituent amino acids on the LCST behavior still remains an open question, the results described in this contribution clearly demonstrate that short, elastin-like peptides are potentially attractive building blocks for a range of materials applications in biomedicine and engineering.
Arabidopsis ABI5 Subfamily Members Have Distinct DNA-Binding and Transcriptional Activities (2002)

A small family of novel basic leucine zipper proteins that includes abscisic acid (ABA)-INSENSITIVE 5 (ABI5) binds to the promoter region of the lea class gene Dc3. The factors, referred to as AtDPBFs (Arabidopsis Dc3 promoter-binding factors), were isolated from an immature seed cDNA library. AtDPBFs bind to the embryo specification and ABA-responsive elements in the Dc3 promoter and are unique in that they can interact with cis-elements that do not contain the ACGT core sequence required for the binding of most other plant basic leucine zipper proteins. Analysis of full-length cDNAs showed that at least five different Dc3 promoter-binding factors are present in Arabidopsis seeds; one of these, AtDPBF-1, is identical to ABI5. As expected, AtDPBF-1/ABI5 mRNA is inducible by exogenous ABA in seedlings. Despite the near identity in their basic domains, AtDPBFs are distinct in their DNA-binding, dimerization, and transcriptional activity.
A Genetic Approach to Idiotypic Vaccination (1993)

Treatment of cancer with vaccines is an attractive prospect, but few tumours express suitable target antigens. With B-cell lymphomas, the idiotypic immunoglobulin (Ig) of the malignant B-cell should provide a suitable target but this requires a vaccine to be created for each patient. We propose a strategy for making such vaccines: first to clone the V genes of the idiotypic Ig, and second to inject the patient with the cloned DNA (genetic immunisation) in order to elicit an immune response against the encoded Ig. We have previously shown that the V genes of the idiotypic Ig can be identified from human lymph node biopsies by polymerase chain reaction amplification, cloning, and sequencing. In this report, we show that anti-idiotypic antibodies can be elicited by direct injection of an expression vector that encodes the V genes of murine antibodies (the V genes of B1.8, a murine hybridoma or of BCL1, a murine lymphoma line). This finding suggests a simple approach to the preparation of idiotypic vaccines for patients with B-cell lymphoma, which also circumvents the need for adjuvants.
Characterization of the Human Ig Heavy Chain Antigen Binding Complementarity Determining Region 3 Using a Newly Developed Software Algorithm, JOINSOLVER (2004)

We analyzed 77 nonproductive and 574 productive human V(H)DJ(H) rearrangements with a newly developed program, JOINSOLVER. In the productive repertoire, the H chain complementarity determining region 3 (CDR3(H)) was significantly shorter (46.7 +/- 0.5 nucleotides) than in the nonproductive repertoire (53.8 +/- 1.9 nucleotides) because of the tendency to select rearrangements with less TdT activity and shorter D segments. Using criteria established by Monte Carlo simulations, D segments could be identified in 71.4% of nonproductive and 64.4% of productive rearrangements, with a mean of 17.6 +/- 0.7 and 14.6 +/- 0.2 retained germline nucleotides, respectively. Eight of 27 D segments were used more frequently than expected in the nonproductive repertoire, whereas 3 D segments were positively selected and 3 were negatively selected, indicating that both molecular mechanisms and selection biased the D segment usage. There was no bias for D segment reading frame (RF) use in the nonproductive repertoire, whereas negative selection of the RFs encoding stop codons and positive selection of RF2 that frequently encodes hydrophilic amino acids were noted in the productive repertoire. Except for serine, there was no consistent selection or expression of hydrophilic amino acids. A bias toward the pairing of 5' D segments with 3' J(H) segments was observed in the nonproductive but not the productive repertoire, whereas V(H) usage was random. Rearrangements using inverted D segments, DIR family segments, chromosome 15 D segments and multiple D segments were found infrequently. Analysis of the human CDR3(H) with JOINSOLVER has provided comprehensive information on the influences that shape this important Ag binding region of V(H) chains.
Prospects for electrically pumped organic lasers (2002)

We examine the effects of nonradiative losses on lasing in crystalline and amorphous organic thin films. In crystalline films, the dominant loss mechanism is singlet-singlet annihilation, and this must be avoided if lasing is to be achieved at practical current densities. The electrically pumped crystalline-tetracene laser structure of Sch\"on et al. [Science 289, 599 (2000)] is studied in detail. Optical and electrical confinement in the bulk structure appears unable to explain the spectral narrowing reported; consequently, we consider electron-hole plasmas, self-focusing at interfaces, and crystal defects as possible sources of the reported phenomena. In amorphous films, lasers are likely to have to operate at current densities $J&lt;1000\mathrm{A}/{\mathrm{cm}}^{2}$ due to a combination of nonradiative losses. The performance of potential lasing materials is quantified by the external quantum efficiency-current--density product, ${\ensuremath{\eta}}_{\mathrm{EXT}}J.$ Electrically pumped lasers require ${\ensuremath{\eta}}_{\mathrm{EXT}}J\ensuremath{\sim}5\mathrm{A}/{\mathrm{cm}}^{2};$ the best amorphous devices currently posses ${\ensuremath{\eta}}_{\mathrm{EXT}}J\ensuremath{\sim}0.3\mathrm{A}/{\mathrm{cm}}^{2}.$ However, we demonstrate that electrically pumped lasing in amorphous materials should be possible using indirect pumping techniques.
Spin Orbit Torque Non-Volatile Flip-Flop for High Speed and Low Energy Applications (2014)

A novel nonvolatile flip-flop based on spin-orbit torque magnetic tunnel junctions (SOT-MTJs) is proposed for fast and ultralow energy applications. A case study of this nonvolatile flip-flop is considered. In addition to the independence between writing and reading paths, which offers a high reliability, the low resistive writing path performs high-speed, and energy-efficient WRITE operation. We compare the SOT-MTJ performances metrics with the spin transfer torque (STT)-MTJ. Based on accurate compact models, simulation results show an improvement, which attains 20× in terms of WRITE energy per bit cell. At the same writing current and supply voltage, the SOT-MTJ achieves a writing frequency 4× higher than the STT-MTJ.