gebhart/patrepeval huggingface dataset:
Improved Digital-to-Analog Conversion Using Multi-Electrode Mach–Zehnder Interferometer (2008)

An improved version of a digital-to-analog converter (DAC) based on a multi-electrode Mach-Zehnder interferometer (MZI) is presented and analyzed. The device described has superior performance regarding both linearity and dynamic range. The improvements are achieved by utilizing a special mapping method between the analog input and the digital sequence applied to the device, and by an optimized sectioning method for the electrodes. Further improvement in linearity is attained by allowing the number of electrodes <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">M</i> to be larger than the number of digitization bits <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</i> ( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">M</i> > <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</i> ). An analytical and systematic method for performing the mapping and selecting the electrodes' sizes is explicitly described and shown to be optimal. A comparison of the proposed approach to previously reported biased MZI reveals that dynamic range and linearity are significantly improved which is translated to increased resolution and reduced quantization errors. It follows from the optimization process that quantization and nonlinearity errors can be reduced to any extent by appropriately increasing the number of electrodes.
The Effect of Plasmin on the Subunit Structure of Human Fibrin (1973)

Non-cross-linked, partially cross-linked, and highly crosslinked human fibrin were each digested with plasmin and the changes in the subunit structures of the degradation products were followed sequentially by sodium dodecyl sulfate polyacrylamide gel electrophoresis.The digestion products of non-cross-linked fibrin were similar to those previously reported for fibrinogen.The digestion products of partially and highly cross-linked fibrin differed somewhat from those of fibrinogen.The a(A) chains of fibrinogen and the (Y chains of non-cross-linked and partially cross-linked fibrin were degraded rapidly to give low molecular weight peptides.The OL polymers of highly cross-linked fibrin were degraded more slowly but also yielded low molecular weight peptides which probably contained cross-links.The /3(B) chain of fibrinogen and the /3 chain in all three types of fibrin yielded a terminal digestion product with a molecular weight of about 44,500.The major digestion products of the y chains of fibrinogen and non-cross-linked fibrin are identical and have molecular weights between 27,000 and 42,000.In contrast, cross-linked y chains are degraded to a species with a molecular weight of 81,000.Fragment E from fibrinogen and Fragment E from fibrin were structurally very similar.Fragment D from fibrinogen and fibrin, however, differed in structure.Structural analyses of the degradation products, which appear during digestion of non-cross-linked, partially cross-linked, and highly cross-linked fibrin, reveal the major features of the digestion pattern of highly cross-linked fibrin by plasmin.Human fibrinogen has a molecular weight of about 330,000 and consists of three pairs of polypeptide subunits called a(A)
Comparative analysis of transcript abundance in Pinus sylvestris after challenge with a saprotrophic, pathogenic or mutualistic fungus (2008)

To investigate functional differences in the recognition and response mechanisms of conifer roots to fungi with different trophic strategies, Pinus sylvestris L. was challenged with a saprotrophic fungus Trichoderma aureoviride Rifai. The results were compared with separate studies investigating pine interactions with a pathogen, Heterobasidion annosum (Fr.) Bref. sensu stricto and an ectomycorrhizal symbiont, Laccaria bicolor Maire (Orton). Global changes in the expression of 2109 conifer genes were assayed 1, 5 and 15 days after inoculation. Gene expression data from a cDNA microarray were analyzed by the 2-interconnected mixed linear model statistical approach. The total number of genes differentially expressed compared with the uninfected control was similar after challenge with the pathogen and the ectomycorrhizal symbiont, but the number of differentially expressed genes increased over time for H. annosum, and decreased for L. bicolor. Inoculation of pine roots with T. aureoviride resulted overall in a much lower number of genes with changed transcript levels compared with inoculation with H. annosum or L. bicolor. Functional classification of the differentially expressed genes revealed that the ectomycorrhizal fungus triggered transient induction of defence-related genes. The response and induction of defence against the pathogen was delayed and the magnitude increased over time. Thus, there were specific transcriptional responses depending on whether the conifer roots were challenged with mutualistic, saprotrophic or pathogenic fungi. This suggests that pine trees are able to recognize diverse fungal species and specifically distinguish whether they are pathogenic, neutral or beneficial microbial agents.
Interferons Regulate the Phenotype of  Wild-type and Mutant Herpes Simplex Viruses In Vivo (1999)

Mechanisms responsible for neuroattenuation of herpes simplex virus (HSV) have been defined previously by studies of mutant viruses in cultured cells. The hypothesis that null mutations in host genes can override the attenuated phenotype of null mutations in certain viral genes was tested. Mutants such as those in infected cell protein (ICP) 0, thymidine kinase, ribonucleotide reductase, virion host shutoff, and ICP34.5 are reduced in their capacity to replicate in nondividing cells in culture and in vivo. The replication of these viruses was examined in eyes and trigeminal ganglia for 1-7 d after corneal inoculation in mice with null mutations (-/-) in interferon receptors (IFNR) for type I IFNs (IFN-alpha/betaR), type II IFN (IFN-gammaR), and both type I and type II IFNs (IFN-alpha/beta/gammaR). Viral titers in eyes and ganglia of IFN-gammaR-/- mice were not significantly different from congenic controls. However, in IFN-alpha/betaR-/- or IFN-alpha/beta/gammaR-/- mice, growth of all mutants, including those with significantly impaired growth in cell culture, was enhanced by up to 1,000-fold in eyes and trigeminal ganglia. Blepharitis and clinical signs of infection were evident in IFN-alpha/betaR-/- and IFN-alpha/beta/gammaR-/- but not control mice for all viruses. Also, IFNs were shown to significantly reduce productive infection of, and spread from intact, but not scarified, corneas. Particularly striking was restoration of near-normal trigeminal ganglion replication and neurovirulence of an ICP34.5 mutant in IFN-alpha/betaR-/- mice. These data show that IFNs play a major role in limiting mutant and wild-type HSV replication in the cornea and in the nervous system. In addition, the in vivo target of ICP34.5 may be host IFN responses. These experiments demonstrate an unsuspected role for host factors in defining the phenotypes of some HSV mutants in vivo. The phenotypes of mutant viruses therefore cannot be interpreted based solely upon studies in cell culture but must be considered carefully in the context of host factors that may define the in vivo phenotype.
Cytokine-like activities of some aminoacyl-tRNA synthetases and auxiliary p43 cofactor of aminoacylation reaction and their role in oncogenesis. (2004)

Multifunctionality of proteins is among mechanisms accounting for the complexity of interactome networks in higher eukaryotes. During oncogenesis and other pathologic conditions many proteins perform additional functions without changes in three dimensional structures. One family of these moonlighting proteins is represented by enzymes and cofactors of aminoacylation reactions, by means of which tRNAs are attached to their cognate amino acids. Tyrosyl-tRNA synthetase (TyrRS), tryptophanyl-tRNA synthetases (TrpRS) and auxiliary factor of mammalian multi-aminoacyl-tRNA synthetases, p43 (precusor of endothelial monocyte activating polypeptide II - EMAP II) upon their release in intracellular environment become proinflammatory cytokines with multiple activities during apoptosis, angiogenesis and inflammation. In addition, these proteins play important role in cancer progression, modulating tumor angiogenesis and its escape from surveillance by immune system.
Synthesis of some N-substituted carbazoles and their larvicidal studies (2005)

Department of Chemistry, Visva-Bharati, Santiniketan-731 235. India <em>E-mail</em>: bpdas2003@yahoo.co.uk Department of Chemistry, Calcutta University, Kolkata-700 009, India <em>Manuscript received 28 October 2003, revised 27 July 2004, accepted 2 September 2004</em> Some <em>N</em>-substituted carbazoles have been synthesized and a comparative larvicidal study has also been done on the larvae of <em>Culex quinquefasciatus</em>.
Banting Lecture 2001 (2002)

Readers of this journal do not need to be reminded of the explosive increase in obesity/type 2 diabetes syndromes and their attendant staggering public health costs that are currently afflicting developed countries. Because of this alarming development and what it portends for the future if left unchecked, the American Diabetes Association, together with its counterparts around the world, as well as the World Health Organization, are faced with the daunting challenge of finding answers to two huge questions. First, what is the pathophysiological basis for these disorders? Second, why is their rate of appearance accelerating so rapidly at this particular juncture of human history, and what, if anything, can we do to intervene? The primary focus of this lecture will be on the first of these issues. I want to emphasize at the outset that I do not plan to dwell exclusively on our own studies in this area. Instead, I shall try to incorporate recent developments from a variety of other laboratories working in the field. Although these will of necessity have to be highly selective, I hope that collectively they will illustrate how we have come to a relatively new and exciting way of thinking about the etiology of type 2 diabetes.

It has been said in literary circles that James Joyce’s Ulysses is probably the most frequently opened and least read book that has ever been published. In a similar vein, I sometimes think that the question of what causes type 2 diabetes might be one of the most frequently asked and least satisfactorily answered in the history of diabetes research. This is not meant to be an arrogant statement, nor indeed does it imply that I have a magical solution to the question at hand. Rather, it simply reflects the fact that at the dawn of …
The removal of 14C labeled endotoxin by activated charcoal. (1979)

Endotoxin shock due to Gram-negative enteric bacteria is of major medical concern with an estimated 100,000 fatalities in the United States per year. An effective therapy for endotoxin shock, particularly in combination with significant liver damage, has not been available to date. Since activated charcoal is known as a universal sorbent, the use of activated charcoal in a hemoperfusion apparatus to remove endotoxin has interesting possibilities. Current assays for endotoxin are inadequate. The Limulus Amoebocyte Lysate (LAL) assay was found to give nonreproducible results within our range of requirements for accuracy. We, therefore, grew Salmonella typhimurium in 14C-labeled glucose to obtain 14C labeled endotoxin. Radiolabeled endotoxin was used to measure the rate of adsorption on activated charcoal. The rates of removal of endotoxin from normal saline, plasma, and whole blood will be presented in graphical form for use in design calculations. This work provides a foundation for encouraging in vivo hemoperfusion experimentation now underway at the University of Oklahoma and the Veteran's Administration Hospital in Oklahoma City.
Glutamate Transporter GLT-1 as a Therapeutic Target for Substance Use Disorders (2015)

The development of new treatments for substance use disorders requires identification of targetable molecular mechanisms. Pathology in glutamatergic neurotransmission system in brain reward circuitry has been implicated in relapse to multiple classes of drugs. Glutamate transporter 1 (GLT-1) crucially regulates glutamatergic signaling by removing excess glutamate from the extrasynaptic space. The purpose of this review is to highlight the effects of addictive drug use on GLT-1 and glutamate uptake, and using GLT-1 as a target in addiction pharmacotherapy. Cocaine, opioids, ethanol, nicotine, amphetamines, and cannabinoids each affect GLT-1 expression and glutamate uptake, and restoring GLT-1 expression with N-acetylcysteine or ceftriaxone shows promise in correcting pre-clinical and clinical manifestations of drug addiction.
Collagen matrices attenuate the collagen-synthetic response of cultured fibroblasts to TGF-β (1995)

Transforming growth factor-beta, a potent modulator of cell function, induces fibroblasts cultured on plastic to increase collagen synthesis. In 5- and 7-day porcine skin wounds, which have minimal to moderate collagen matrix, respectively, transforming growth factor-beta and type I procollagen were coordinately expressed throughout the granulation tissue. However, in 10-day collagen-rich granulation tissue type I procollagen expression diminished despite persistence of transforming growth factor-beta. To investigate whether collagen matrix attenuates the collagen-synthetic response of fibroblasts to transforming growth factor-beta, we cultured human dermal fibroblasts in conditions that simulate collagen-rich granulation tissue. Therefore, human dermal fibroblasts were suspended in attached collagen gels and collagen and noncollagen production was assayed in the absence and presence of transforming growth factor-beta. Although transforming growth factor-beta stimulated collagen synthesis by fibroblasts cultured in the collagen gels, these fibroblasts consistently produced less collagen than similarly treated fibroblasts cultured on plastic. This phenomenon was not secondary to nonspecific binding of transforming growth factor-beta to the collagen matrix. Fibroblasts cultured in a fibrin gel responded to transforming growth factor-beta similarly to fibroblasts cultured on plastic. Using immunofluorescence probes to type I procollagen, we observed that transforming growth factor-beta increased type I procollagen expression in most fibroblasts cultured on plastic, but only in occasional fibroblasts cultured in collagen gels. From these data we conclude that collagen matrices attenuate the collagen synthetic response of fibroblast to transforming growth factor-beta in vitro and possibly in vivo.
A gene encoding a sphingolipid biosynthesis enzyme determines the sensitivity of Saccharomyces cerevisiae to an antifungal plant defensin from dahlia ( Dahlia merckii ) (2000)

We have previously identified a Saccharomyces cerevisiae mutant that is markedly more resistant than wild-type to Dahlia merckii antimicrobial peptide 1 (DmAMP1), an antifungal plant defensin isolated from seeds of dahlia (Dahlia merckii). A complementation approach was followed that consisted of the introduction of a genomic library of DmAMP1-sensitive wild-type yeast into the DmAMP1-resistant yeast mutant and screening for restored sensitivity to DmAMP1. The gene determining sensitivity of S. cerevisiae to DmAMP1 was identified as IPT1, a gene encoding an enzyme involved in the last step of the synthesis of the sphingolipid mannose-(inositol-phosphate)(2)-ceramide. Strains with a nonfunctional IPT1 allele lacked mannose-(inositol-phosphate)(2)-ceramide in their plasma membranes, bound significantly less DmAMP1 compared with wild-type strains, and were highly resistant to DmAMP1-mediated membrane permeabilization. All of these phenotypic deviations could be restored by reintroduction of a functional IPT1 gene. Our data support a model in which membrane patches containing sphingolipids act as binding sites for DmAMP1 or, alternatively, are required to anchor membrane or cell wall-associated proteins, which themselves interact with DmAMP1.
Mammalian Transcription Factor ATF6 Is Synthesized as a Transmembrane Protein and Activated by Proteolysis in Response to Endoplasmic Reticulum Stress (1999)

The unfolded protein response (UPR) controls the levels of molecular chaperones and enzymes involved in protein folding in the endoplasmic reticulum (ER). We recently isolated ATF6 as a candidate for mammalian UPR-specific transcription factor. We report here that ATF6 constitutively expressed as a 90-kDa protein (p90ATF6) is directly converted to a 50-kDa protein (p50ATF6) in ER-stressed cells. Furthermore, we showed that the most important consequence of this conversion was altered subcellular localization; p90ATF6 is embedded in the ER, whereas p50ATF6 is a nuclear protein. p90ATF6 is a type II transmembrane glycoprotein with a hydrophobic stretch in the middle of the molecule. Thus, the N-terminal half containing a basic leucine zipper motif is oriented facing the cytoplasm. Full-length ATF6 as well as its C-terminal deletion mutant carrying the transmembrane domain is localized in the ER when transfected. In contrast, mutant ATF6 representing the cytoplasmic region translocates into the nucleus and activates transcription of the endogenous GRP78/BiP gene. We propose that ER stress-induced proteolysis of membrane-bound p90ATF6 releases soluble p50ATF6, leading to induced transcription in the nucleus. Unlike yeast UPR, mammalian UPR appears to use a system similar to that reported for cholesterol homeostasis.
New types of organometallic oxo complexes containing tungsten (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNew types of organometallic oxo complexes containing tungstenPeter Legzdins, Steven J. Rettig, and Luis SanchezCite this: Organometallics 1985, 4, 8, 1470–1471Publication Date (Print):August 1, 1985Publication History Published online1 May 2002Published inissue 1 August 1985https://doi.org/10.1021/om00127a033RIGHTS & PERMISSIONSArticle Views101Altmetric-Citations32LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (287 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Resistance Tests and Genetic Resources for Breeding Fusarium Root Rot Resistant Lettuce (2004)

Using a method for testing a varietal resistance of lettuce to fusarium root rot, we evaluated the resistance of genetic resources of lettuce gathered from Japan and abroad as an aid to our breeding progrom. Seeds were sown in a mixture of nursery soil of pathogenic fungus-cultured bran and vermiculite (bran:vermiculite = 1:1.5, v/v) and commercial horticultural nursery soil (mixing ratio: 1/10∼1/40, w/w), that included more than 108 cells per ml of Fusarium oxysporum f. sp. lactucae. The seeded plug trays with the inoculated soil were kept for 30 to 40 days at 15 °C to 35 °C (mean of 25 °C ) in a glasshouse under natural daylength. At the end of incubation period, seeding were indexed for resistance to fusarium root rot. Resistance tests were conducted on 78 accessions of genotypes from Japan, and 77 accessions which were mainly crisp-type lettuce gathered from abroad between 1999 and 2000. Regardless of the sources of these genotypes, large differences were seen in disease severity among the genotypes. Among those from Japan, many of the 'Vanguard' type varieties possessed more resistance to isolate SB1-1 (Race 1) and 'V Lettuce' were highly resistance to isolate SB1-1, whereas 'Empire' types, 'Kikugawa 102' and 'Blizzard'were highly susceptible. However, many 'Vanguard' type varieties, 'V Lettuce' were highly susceptible to isolate F9501 (Race 2). while 'Kikugawa 102' and 'Blizzard' possessed highly resistance to isolate F9501. Compared to those genetic resources gathered from Japan, a larger number of materials from abroad showed resistance. 'Batavia Tezier' and 'Batavia Blonde de Paris' tested to be resistant to both SB1- 1 and F9501.
RETINOID‐BINDING PROTEINS IN PLASMA AND IN CELLS* (1981)

Much has been learned during the past decade about the specific retinoid-binding proteins that exist in plasma, and in the intracellular compartment in a number of tissues. Vitamin A is mobilized from liver stores and transported in plasma in the form of the lipid alcohol retinol, bound to a specific transport protein, retinol-binding protein (RBP). A great deal is now known about the chemical structure, metabolism, and biological roles of RBP. Vitamin A mobilization from the liver is highly regulated by factors that control the rates of RBP production and secretion. Retinol deficiency specifically blocks the secretion of RBP, which can then be rapidly stimulated by intravenous retinol repletion. The cellular and molecular mechanisms that mediate these phenomena are under investigation. Delivery of retinol to peripheral tissues appears to involve specific cell surface receptors for RBP. The retinol so delivered enters the target cell, where it may become associated with the intracellular binding protein for retinol (CRBP). A number of tissues of rats, humans, and other species contain soluble proteins with binding specificity for retinol (CRBP) or for retinoic acid (CRABP). These proteins have been purified from several tissues and partly characterized. They differ in a number of ways from plasma RBP, and differ from each other in regard to binding specificity and immunoreactivity. It has been suggested that these intracellular proteins may play a direct role in the biological expression of vitamin A activity in the cell. Studies are in progress to explore this and other possibilities.
Effective detergent/lipid ratios in the solubilization of phosphatidylcholine vesicles by Triton X‐100 (1992)

Effective detergent:lipid ratios (i.e. molar ratios in the mixed aggregates, vesicles or micelles) have been estimated for the solubilization of phosphatidylcholine vesicles by Triton X-100. Effective molar ratios are given for both the onset and the completion of bilayer solubilization; small unilamellar, large unilamellar and multilamellar vesicles have been used. Effective detergent:lipid ratios are independent of phospholipid concentration, and their use allows a deeper understanding of membrane-surfactant interactions.