gebhart/patrepeval huggingface dataset:
Toxoplasma gondii peptide ligands open the gate of the HLA class I binding groove (2016)

HLA class I presentation of pathogen-derived peptide ligands is essential for CD8+ T-cell recognition of Toxoplasma gondii infected cells. Currently, little data exist pertaining to peptides that are presented after T. gondii infection. Herein we purify HLA-A*02:01 complexes from T. gondii infected cells and characterize the peptide ligands using LCMS. We identify 195 T. gondii encoded ligands originating from both secreted and cytoplasmic proteins. Surprisingly, T. gondii ligands are significantly longer than uninfected host ligands, and these longer pathogen-derived peptides maintain a canonical N-terminal binding core yet exhibit a C-terminal extension of 1-30 amino acids. Structural analysis demonstrates that binding of extended peptides opens the HLA class I F' pocket, allowing the C-terminal extension to protrude through one end of the binding groove. In summary, we demonstrate that unrealized structural flexibility makes MHC class I receptive to parasite-derived ligands that exhibit unique C-terminal peptide extensions.
Reactions of nitric oxide with mitochondrial cytochrome c: a novel mechanism for the formation of nitroxyl anion and peroxynitrite (1998)

The aerobic reactions of nitric oxide with cytochrome c were analysed. Nitric oxide (NO) reacts with ferrocytochrome c at a rate of 200 M-1 s-1 to form ferricytochrome c and nitroxyl anion (NO-). Ferricytochrome c was detected by optical spectroscopy; NO- was detected by trapping with metmyoglobin (Mb3+) to form the EPR-detectable Mb-nitrosyl complex, and by the formation of dimers in yeast ferrocytochrome c via cross-linking of the free cysteine residue. The NO- formed subsequently reacted with oxygen to form peroxynitrite, as measured by the oxidation of dihydrorhodamine 123. NO binds to ferricytochrome c to form the ferricytochrome c-NO complex. The on-rate for this reaction is 1.3+/-0.4x10(3) M-1.s-1, and the off-rate is 0.087+/-0.054 s-1. The dissociation constant (Kd) of the complex is 22+/-7 microM. These reactions of NO with cytochrome c are likely to be relevant to mitochondrial metabolism of NO. Ferricytochrome c can act as a reversible sink for excess NO in the mitochondria. The reduction of NO to NO- by ferrocytochrome c may play a role in the irreversible inhibition of mitochondrial oxygen consumption by peroxynitrite. It is generally assumed that peroxynitrite would be formed in mitochondria via the reaction of NO with superoxide. The finding that NO- is formed from the reaction of NO and ferrocytochrome c provides a means of producing peroxynitrite in the absence of superoxide, via the reaction of NO- with oxygen.
Rapid Regeneration of Lettuce from Suspension Culture (1992)

An efficient method for the regeneration of shoots directly from cell suspensions of three commercial cultivars of lettuce (Lactuca sativa L. cv. Great Lakes 659-700, Salad Bowl, and Prize Head) is described. Cell suspensions were prepared by osterizing cotyledon-derived callus for 60 seconds. The effects of callus quality, light intensity, carbohydrate type and concentration, auxins, and cytokinins on cell growth and differentiation in the suspension culture were examined. Among these factors, callus quality and carbohydrates were the most critical. The optimal medium for regeneration of shoots in suspension culture was SH (Schenk and Hilderbrandt) basal medium containing 1000 mg myo -inositol/liter, 1.5% glucose, 0.44 μ m BA, and 0.54 μ m NAA. The pH of the medium was adjusted to 5.8. Under such condition, hundreds of shoots could be produced from 50 to 55 mg (dry wt) of cell aggregates within 2 weeks. Chemical names used: α-] naphthaleneacetic acid (NAA); indole3-acetic acid (IAA); 6-benzylaminopurine (BA).
Early and Strong Immune Responses Are Associated with Control of Viral Replication and Recovery in Lassa Virus-Infected Cynomolgus Monkeys (2009)

Lassa virus causes a hemorrhagic fever endemic in West Africa. The pathogenesis and the immune responses associated with the disease are poorly understood, and no vaccine is available. We followed virological, pathological, and immunological markers associated with fatal and nonfatal Lassa virus infection of cynomolgus monkeys. The clinical picture was characterized by fever, weight loss, depression, and acute respiratory syndrome. Transient thrombocytopenia and lymphopenia, lymphadenopathy, splenomegaly, infiltration of mononuclear cells, and alterations of the liver, lungs, and endothelia were observed. Survivors exhibited fewer lesions and a lower viral load than nonsurvivors. Although all animals developed strong humoral responses, antibodies appeared more rapidly in survivors and were directed against GP(1), GP(2), and NP. Type I interferons were detected early after infection in survivors but only during the terminal stages in fatalities. The mRNAs for CXCL10 (IP-10) and CXCL11 (I-TAC) were abundant in peripheral blood mononuclear cells and lymph nodes from infected animals, but plasma interleukin-6 was detected only in fatalities. In survivors, high activated-monocyte counts were followed by a rise in the total number of circulating monocytes. Activated T lymphocytes circulated in survivors, whereas T-cell activation was low and delayed in fatalities. In vitro stimulation with inactivated Lassa virus induced activation of T lymphocytes from all infected monkeys, but only lymphocytes from survivors proliferated. Thus, early and strong immune responses and control of viral replication were associated with recovery, whereas fatal infection was characterized by major alterations of the blood formula and, in organs, weak immune responses and uncontrolled viral replication.
Editor's Note (1996)

Doctor of History Larisa Georgievna Zakharova is professor of history at Moscow University. Her book Samoderzhavie i otmena krepostnogo prava v Rossii, 1856-1861 established Professor Zakharova as one of Russia's foremost authorities on the Great Reforms and autocratic politics. More recently she has coedited Russia's Great Reforms, 1855-1881 and 1857-1861: Perepiska Imperatora Aleksandra II s Velikim Kniazem Konstantinom Nikolaevichem. Dnevnik Velikogo Kniazia Konstantina Nikolaevicha. A member of the advisory board of this journal, she is familiar to our readers. The Fall 1987 issue presented an abridgement of her book on autocracy and emancipation; the Spring 1991 issue contained her article "Autocracy, Bureaucracy, and the Reforms of the 1860s in Russia"; and the Winter 1993-94 issue included her portrait of Alexander II.
A mouse lymphoma cell line resistant to the leukoagglutinating lectin from Phaseolus vulgaris is deficient in UDP-GlcNAc: alpha-D-mannoside beta 1,6 N-acetylglucosaminyltransferase. (1982)

A UDP-G1cNAc:a-mannoside p1,6 N-acetylglucosaminyltransferase was identified in cell-free preparations from the mouse lymphoma cell line BW5147.A novel assay employing concanavalin A-Sepharose, lentil lectin-Sepharose, and radioiodinated glycopeptide acceptors was devised to specifically measure the activity of this enzyme.The enzyme transfers N-acetylglucosamine to the C-6 position of a-linked mannose residues and utilizes as acceptors biantennary Asnlinked oligosaccharides containing N-acetylglucosamine, but not sialic acid or galactose, at the nonreducing termini.The product of the enzyme is a triantennary glycopeptide.The level of this enzyme activity was markedly decreased in a mouse lymphoma cell line (BW5147-PHAR2.1),which has previously been shown to be resistant to the cytotoxic effects of the leukoagglutinating lectin (L-PHA) from Phaseolus vulgaris (Trowbridge, I.
Augmentation of respiratory mast cell secretion of histamine caused by vagus nerve stimulation during antigen challenge. (1986)

We studied the effect of vagus nerve stimulation on the mast cell secretion of histamine after intraarterial (i.a.) administration of Ascaris suum antigen (AA) into the bronchial circulation of 10 randomly selected, natively allergic dogs in vivo. Respiratory mast cell response was measured as the arteriovenous difference (AVd) in histamine concentration across the bronchus. Plasma histamine concentration was determined simultaneously from right atrium, right ventricle, and femoral artery 60 and 15 sec before and 15, 30, 45, 60, 75, and 90 sec after i.a. injection of sham (Kreb-Henseleit) diluent, 1:100, and 1:30 concentrations of AA. The mean AVd in plasma histamine for five parasympathetically blocked animals (neural blockade with hexamethonium and beta-adrenergic blockade with propranolol) was 1.28 +/- 0.61 ng/ml (sham), 5.16 +/- 19.7 ng/ml (1:100 AA), and 36.6 +/- 11.1 ng/ml (1:30 AA). Substantial augmentation was obtained when AA was administered during parasympathetic stimulation in five other animals (beta-adrenergic blockade, no neural blockade), which was caused by continuous bilateral electrical stimulation of the vagus nerves. A mean AVd in plasma histamine of 110 +/- 27.6 ng/ml was obtained after 1:100 AA (p less than 0.001 vs parasympathetic blockade) and 166 +/- 32.4 ng/ml for 1:30 AA (p less than 0.001 vs parasympathetic blockade). Parasympathetic stimulation alone did not cause secretion of histamine. In contrast to the AVd response, parasympathetic stimulation did not augment nonrespiratory mast cell secretion after AA challenge. We conclude that vagus nerve stimulation augments secretion of histamine from respiratory mast cells during antigen challenge. We demonstrate that parasympathetic stimulation may potentiate the response to antigen challenge in central airways through augmented mast cell secretion of mediator.
Influence of the Heating Rate and the Type of Catalyst on the Formation of Key Intermediates and on the Generation of Gases During Hydropyrolysis of Glucose in Supercritical Water in a Batch Reactor (2003)

To understand the influence of experimental conditions on the chemistry of biomass degradation in supercritical water, the effect of heating rate and of different catalysts (1 wt % of Raney nickel and 0.5 wt % K2CO3) on the product distribution during hydropyrolysis of glucose is investigated. Glucose in aqueous solution (5 wt %) is selected as a model compound for cellulosic biomass. The heating rates are 1 or 3 K/min up to 500 °C, and then, the reactor is kept at this temperature for 1 h. Despite the long reaction time of 1 h at 500 °C, the presence of catalysts has an significant influence on intermediates of glucose gasification such as phenols or furfurals. The influence of catalyst and the heating rate on these intermediates and the product yields points to the assumption that the chemical processes during heating have a drastic effect on the results of the gasification process at 500 °C.
Multimedia Retrieval and Delivery: Essential Metadata Challenges and Standards (2008)

Multimedia information retrieval (MIR) and delivery plays an important role in many application domains due to the increasing need to identify, filter, and manage growing amounts of data, notably multimedia information. To efficiently manage and exchange multimedia information, interoperability between coded data and metadata is required and standardization is central to achieving the necessary level of interoperability. In the context of this paper, the term retrieval refers to the process by which a user, human or machine, identifies the content it needs, and the term delivery refers to the adaptive transport and consumption of the identified content in a particular context or usage environment. Both the retrieval and delivery processes may require content and context metadata. This paper will argue that maximum quality of experience depends not only on the content itself (and thus content metadata) but also on the consumption conditions (thus context metadata). Additionally, the rights and protection conditions have become critically important in recent years, especially with the explosion of electronic music commerce and different ldquoshoppingrdquo conditions. This paper will review existing multimedia standards related to information retrieval and adaptive delivery of multimedia content, emphasizing the need for such standards, and will show how these standards can help the development, dissemination, and valorization of MIR research results. Moreover, it will also discuss limitations of the current standards and anticipate what future standardization activities are relevant and needed. Due to space limitations, the paper will mainly concentrate on MPEG standards although many other relevant standards are also reviewed and discussed.
A WWW Implementation of National Recommendations for Protecting Electronic Health Information (1997)

In March of 1997, the National Research Council (NRC) of the National Academy of Sciences issued the report, "For the Record: Protecting Electronic Health Information." Concluding that the current practices at the majority of health care facilities in the United States are insufficient, the Council delineated both technical and organizational approaches to protecting electronic health information. The Beth Israel Deaconess Medical Center recently implemented a proof-of-concept, Web-based, cross-institutional medical record, CareWeb, which incorporates the NRC security and confidentiality recommendations. We report on our WWW implementation of the NRC recommendations and an initial evaluation of the balance between ease of use and confidentiality.
Multi-scale quantification of leaching performance using X-ray tomography (2016)

The performance of heap leaching is dictated by a large number of processes acting at a wide range of length scales. One important scale is that of the individual particles, where the interaction between the rate kinetics at the surfaces of the individual mineral grains and the mass transport through the particle combine to give the overall apparent particle scale kinetics. It has been recognised for a long time that variability in the mineralogy, size and spatial distribution of the mineral grains within the particle are likely to have a large effect on the leach performance and its variability and thus, ultimately, the performance of the heap. In this paper a new method for quantifying this behaviour and its variability at scales from the particle through to the grain and down to the surface kinetics is presented. This method is based on the use of a series of XMT (also called micro-CT) images of a column taken at regular intervals over 168 days of leaching. The key development in the analysis of this data is an algorithm that has allowed every single one of the hundreds of thousands of mineral grains within the column to be individually tracked across all the time points as they undergo dissolution. This has allowed the dependency of the mineral grain leach rate on its size and position in the particle to be decoupled from one another. It also meant that the variability in the surface kinetics of the grains could be assessed, with mineralogical variability being the key source of this variability. We demonstrate that understanding and quantifying this underlying kinetic variability is important as it has a major impact on the time evolution of the average kinetics of the leaching.
A peptide derived from α-fetoprotein prevents the growth of estrogen-dependent human breast cancers sensitive and resistant to tamoxifen (2002)

An 8-mer peptide (EMTOVNOG) derived from alpha-fetoprotein was compared with tamoxifen for activity against growth of human breast cancer xenografts implanted in immune-deficient mice. Both peptide and tamoxifen prevented growth of estrogen-receptor-positive MCF-7 and T47D human breast cancer xenografts. A subline of MCF-7, made resistant to tamoxifen by a 6-month exposure to this drug in culture, was found to be resistant to tamoxifen in vivo. Peptide completely prevented the xenograft growth of this tamoxifen-resistant subline of MCF-7. Neither peptide nor tamoxifen was effective in slowing the xenograft growth of the estrogen-receptor-negative MDA-MB-231 human breast cancer. A worrisome side effect of tamoxifen is its hypertrophic effect on the uterus. In this study, tamoxifen was shown to stimulate the growth of the immature mouse uterus in vivo, and the peptide significantly inhibited tamoxifen's uterotrophic effect. The mechanism of action of peptide is different from that of tamoxifen in that the peptide does not interfere with the binding of [(3)H]estradiol to the estrogen receptor. In conclusion, alpha-fetoprotein-derived peptide appears to be a novel agent that interferes with the growth of tamoxifen-sensitive as well as tamoxifen-resistant estrogen-receptor-positive human breast cancers; it inhibits the uterotrophic side effect of tamoxifen and, thus, it may be useful in combination with or in place of tamoxifen for treatment of estrogen-receptor-positive human breast cancers.
Introduction of local memory elements in instruction set extensions (2004)

Automatic generation of Instruction Set Extensions (ISEs), to be executed on a custom processing unit or a coprocessor is an important step towards processor customization. A typical goal of a manual designer is to combine a large number of atomic instructions into an ISE satisfying microarchitectural constraints. However, memory operations pose a challenge for previous ISE approaches by limiting the size of the resulting instruction. In this paper, we introduce memory elements into custom units which result in ISEs closer to those sought after by the designers. We consider two kinds of memory elements for mapping to the specialized hardware: small hardware tables and architecturally-visible state registers. We devised a genetic algorithm to specifically exploit opportunities of introducing memory elements during ISE generation. Finally, we demonstrate the effectiveness of our approach by a detailed study of the variation in performance, area and energy in the presence of the generated ISEs, on a number of MediaBench, EEMBC and cryptographic applications. With the introduction of memory, the average speedup varied from 2.7X to 5X depending on the architectural configuration with a nominal area overhead. Moreover, we obtained an average energy reduction of 26% with respect to a 32-KB cache.
G‐CSF‐mobilized peripheral blood progenitor cells for allogeneic transplantation: safety, kinetics of mobilization, and composition of the graft (1994)

Allogeneic transplantation of peripheral blood progenitor cells (PBPC) makes the general anaesthesia of the donor unnecessary and may result in more rapid engraftment and faster recovery of the immune system. We have studied G-CSF-mediated PBPC mobilization in healthy donors and analysed the cellular composition of the resulting PBPC grafts. PBPC grafts were obtained from nine healthy donors (18-67 years old) for allogeneic or syngeneic transplantation. Six donors received 10 micrograms/kg G-CSF per day, the others 5-6 micrograms/kg. Mobilization and harvesting were well tolerated except for moderate bone pain which occurred in all donors primed with 10 micrograms/kg. With 10 micrograms/kg, a 31-fold (9-62) enrichment of circulating CD34+ cells was observed with peak values constantly occurring on day 5 after the start of G-CSF administration. Starting harvest on day 5, one to three collections on consecutive days yielded 5.5 x 10(6)/kg (0.9-10.7) CD34+ cells, 219 x 10(6)/kg (106-314) T cells, and 34 x 10(6)/kg (23-67) NK cells per 10 litres leukapheresis volume. Altogether, PBPC grafts contained 3 times more CD34+ cells, 7 times more T cells, and 20 times more NK cells than five allogeneic marrow grafts that were analysed for comparison. The yield of CD34+ cells per 10 litres apheresis volume as well as the height of the CD34+ peak in peripheral blood were inversely correlated to the age of the donor. In the donors primed with 5-6 micrograms/kg G-CSF the increase of circulating CD34+ cells (4-7-fold enrichment) and the CD34+ cell yield per 10 litres leukapheresis volume (1 x 10(6)/kg [0.8-2.2]) was much smaller compared with the 10 micrograms/kg group. In conclusion, sufficient amounts of PBPC capable of restoring haemopoiesis in allogeneic recipients can be mobilized safely by administration of G-CSF (10 micrograms/kg s.c. for 5 d) in healthy donors, and harvested with one or two leukapheresis procedures. Whether the large numbers of T-cells and NK cells that are contained in the collection products may influence graft-versus-host and graft-versus-leukaemia reactivities of PBPC grafts remains to be determined.
Photoconductor fatigue. 3. Effect of polymer on the photooxidation of the charge-transport layer of organic layered photoconductors (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhotoconductor fatigue. 3. Effect of polymer on the photooxidation of the charge-transport layer of organic layered photoconductorsJ. Pacansky and R. J. WaltmanCite this: Chem. Mater. 1991, 3, 5, 912–917Publication Date (Print):September 1, 1991Publication History Published online1 May 2002Published inissue 1 September 1991https://doi.org/10.1021/cm00017a029Request reuse permissions Article Views54Altmetric-Citations3LEARN 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 (701 KB) Get e-Alertsclose Get e-Alerts
Catalytic asymmetric allylation of aldehydes (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCatalytic asymmetric allylation of aldehydesGary E. Keck, Kenneth H. Tarbet, and Leo S. GeraciCite this: J. Am. Chem. Soc. 1993, 115, 18, 8467–8468Publication Date (Print):September 1, 1993Publication History Published online1 May 2002Published inissue 1 September 1993https://pubs.acs.org/doi/10.1021/ja00071a074https://doi.org/10.1021/ja00071a074research-articleACS PublicationsRequest reuse permissionsArticle Views5495Altmetric-Citations495LEARN 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-Alertsclose Get e-Alerts