gebhart/patrepeval huggingface dataset:
Cross‐Reactive Antibodies Prevent the Lethal Effects ofStaphylococcus aureusSuperantigens (1999)

The exotoxins produced by Staphylococcus aureus, staphylococcal enterotoxins (SE) A-E and toxic shock syndrome toxin (TSST)-1, which are associated with serious diseases, including food poisoning and toxic shock syndrome, are termed superantigens (SAgs). To examine whether common antigenic epitopes were present and whether vaccination with 1 bacterial SAg could protect against challenge with a different SE or TSST-1, mice were vaccinated with SEA, SEB, SEC1, or TSST-1 individually or in combination. Mice injected with a single toxin developed high antibody titers against other SAgs. Marked improvement in survival was observed when immunized mice were challenged with a heterologous toxin. Mice vaccinated with a mixture of toxins were fully protected against 1 or multiple toxin challenges, indicating no interference effects of multivalent vaccinations. More importantly, higher titers were found against each SAg with the multivalent vaccination than with injection with a single SAg. Thus, immunizations with 1 SAg can induce cross-protective antibodies to heterologous SAgs, and multicomponent vaccination can enhance antibody responses against each bacterial SAg.
The A′ and F′ Pockets of Human CD1b Are Both Required for Optimal Presentation of Lipid Antigens to T Cells (2001)

CD1 proteins are unique in their ability to present lipid Ags to T cells. Human CD1b shares significant amino acid homology with mouse CD1d1, which contains an unusual putative Ag-binding groove formed by two large hydrophobic pockets, A' and F'. We investigated the function of the amino acid residues that line the A' and F' pockets of CD1b by engineering 36 alanine-substitution mutants and analyzing their ability to present mycobacterial glycolipid Ags. Two lipid Ags presented by CD1b were studied, a naturally occurring glucose monomycolate (GMM) isolated from mycobacteria, which contains two long alkyl chains (C54-C62 and C22-C24) and synthetic GMM (sGMM), which includes two short alkyl chains (C18 and C14). We identified eight residues in both the A' and F' pockets that were involved in the presentation of both GMM and sGMM to T cells. Interestingly, four additional residues located in the distal portion of the A' pocket were required for the optimal presentation of GMM, but not sGMM. Conversely, nine residues located between the center of the groove and the F' pocket were necessary for the optimal presentation of sGMM, but not GMM. These data indicate that both the A' and F' pockets of human CD1b are required for the presentation of lipid Ags to T cells.
Abstract 3457: Novel polymeric implants for low-dose, continuous exposure to carcinogens (2010)

Abstract Current practices to determine the DNA-damaging and carcinogenicity potential of a chemical generally involves treatment of rodents with single or multiple bolus doses. However, humans are almost always exposed to low doses continuously. Thus, carcinogenic potential of a chemical has relied on extrapolation of doses tested in pre-clinical studies. What is needed is a low-dose continuous-exposure system to mimic the human-exposure scenario. We recently described novel polymeric implants capable of providing controlled release of compounds continuously for long duration. When implants of polycaprolactone: F68 (9:1) embedded with benzo[a]pyrene (BP) were grafted subcutaneously in female rats, we found nearly constant levels of DNA adducts over one month period in the liver and lung upon analysis by 32P-postlabeling assay. In this study we describe tissue DNA adduct accumulation over extended periods, and effect of low-dose continuous treatment on cytochrome P450s associated with BP metabolism. Groups of female S/D rats received either no treatment or received subcutaneous sham implants or implants embedded with BP. Animals were euthanized at 1, 2, 4 and 25 weeks and different tissues were collected. Analysis of the liver and lung by 32P-postlabeling showed that the adduct burden in lung (14 - 16 adducts/109 nucleotides) was somewhat higher than in liver (11 - 12 adducts/109 nucleotides) over the 30 day period. At the end of the study, the adduct levels in the liver remained practically at the steady-state (17 adducts/109 nucleotides). However, in the lung, the adduct levels increased by nearly two fold (31 adducts/109 nucleotides). These data suggest that over extended period, the highest adduct accumulation occurred in the lung presumably due to tissue-specific differences in adduct formation and/or removal. To determine if the steady-state adduct levels were related to steady modulation of CYPs, we analyzed CYP1A1 and CYP1B1 at both mRNA and protein levels. It was found that after 1 week of treatment, both CYP1A1 and CYP1B1 were substantially over expressed at both RNA and protein levels and remained up-regulated up to 4 weeks analyzed thus far. The steady-state up-regulation of these CYPs and tissue DNA adduction in this study is consistent with our cigarette smoke exposure study in which female A/J mice showed sustained over expression of CYP1A1 and CYP1B1 during the smoke-exposure period of three months. In summary, the polymeric implants provide a low-dose continuous (“24/7”)-exposure system to determine DNA-damaging and carcinogenicity potential of environmental carcinogens. This sustained-release exposure system is also relevant to the human scenario for determining efficacy of chemopreventive agents. (Supported from CA-118114, CA-125152 and Agnes Brown Duggan Endowment) Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3457.
A 0.04 cc Power Amplifier Module with Fully Integrated Passives in a Hybrid LTCC Substrate for 5-GHz Wireless LANs (2002)

A compact power amplifier (PA) module using a novel hybrid low-temperature co-fired ceramic (LTCC) substrate has been developed for 5-GHz wireless LANs (WLANs). Passive components were embedded in the multi-layer LTCC substrate, which was laminated with three types of dielectrics. The hybrid substrate makes it possible to reduce component area and minimize RF coupling among the components. These improvements allowed us to integrate matching and bias networks within a compact 5 × 5 × 1.4 mm3 (= 0.04 cc) module size. The PA module was accurately designed using a passive component library developed based on EM (electromagnetic) simulation. The fabricated module exhibited power performance sufficient for 5-GHz WLANs, i.e., - linear gain of 25 dB and output 1-dB compression power (P1dB) of 21 dBm with power added efficiency (PAE) of 19%. This is the first report of a PA module with fully embedded matching networks in an LTCC substrate for 5-GHz Wireless LANs.
Higher-dose rifampin for the treatment of pulmonary tuberculosis: a systematic review. (2011)

Historical trials suggest that higher than standard RMP dosing results in improved culture conversion rates. Phase 2 and 3 clinical trials evaluating higher doses of RMP and other rifamycins are needed to confirm efficacy and assure tolerability. Pharmacokinetic studies will be needed to inform the development of such trials.
Constrained Sensitivity Analysis for Reactor Physics Problems (2020)

This summary introduces an algorithm for completing sensitivity analysis that respects linear constraints placed on the associated model’s input parameters. With constraints&lt;br/&gt;present, the degrees of freedom of input parameters are reduced, and any changes, e.g., parameter perturbations, must respect these constraints. This summary motivates the&lt;br/&gt;need for this algorithm, overviews the theoretical results, and offers representative numerical experiments. The original work focuses on the sensitivity of corewide keff [1]. In this summary, a virtual bare fast reactor whose core has three different fuel materials (U235, U238, Pu239) is employed to demonstrate the performance of the proposed algorithm. The nominal three-group constants of fast reactors are used in the criticality analysis [2]. The objective is to calculate the sensitivity of k∞ with respect to the volumetric ratio of fissile materials (U235, U238, Pu239) in a multi-group format. The constraint of this analysis is that the sum of the volumetric composition ratio of the fissile materials is equal to unity.
A Tissue-Engineered Stent for Cell-Based Vascular Gene Transfer (2002)

Cell-based gene transfer using a stent platform would provide a significant advantage in terms of site-specific gene expression in the vasculature. The current study presents a novel stent design that allows stable in vivo transgene expression over a 4-week period in the vasculature. A mesh-stent coated with fibronectin provided an excellent platform for adherent porcine smooth muscle cells (SMC). Autologous porcine SMC were stably transduced with a plasmid encoding green fluorescence protein (GFP), seeded at high density in the mesh-stent, and deployed in the porcine coronary artery. Stable in vivo GFP expression within the mesh-stent (5.2 x 10(5) GFP-positive cells/cm(2) mesh) was demonstrated 1 month after implantation in the porcine coronary artery by fluorescence microscopy and flow cytometry. No significant change in GFP positive cell number within the stent occurred over a 1-month period in vivo when compared to preinsertion. Angiographic and histologic analysis revealed mild neointimal proliferation and no inflammatory infiltrate in the stented segment. This study has implications for treatment of cardiovascular and other diseases where long-term cell-based delivery of transgene is a desirable therapeutic option.
Design of a CMOS track-and-hold amplifier for a 6-bit 1-GS/s interpolating flash ADC (2011)

The design of a CMOS track-and-hold amplifier (THA) for a 6-bit 1-GS/s interpolating flash ADC is presented. Since the goal of the overall project was to determine the performance of a new ADC calibration architecture, the THA was prohibited from being the limiting factor in the performance of the ADC; consequently the THA was required to have at least 56dB of signal-to-noise and distortion ratio (SNDR) at the Nyquist frequency. The THA architecture, design methodology, and supporting simulation results will be presented.
Influence of stereochemistry on activity and binding modes for C2 symmetry-based diol inhibitors of HIV-1 protease (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTInfluence of stereochemistry on activity and binding modes for C2 symmetry-based diol inhibitors of HIV-1 proteaseMadhusoodan V. Hosur, T. Narayana Bhat, Dale J. Kempf, Eric T. Baldwin, Beishan Liu, Sergei Gulnik, Norman E. Wideburg, Daniel W. Norbeck, Krzysztof Appelt, and John W. EricksonCite this: J. Am. Chem. Soc. 1994, 116, 3, 847–855Publication Date (Print):February 1, 1994Publication History Published online1 May 2002Published inissue 1 February 1994https://doi.org/10.1021/ja00082a004Request reuse permissionsArticle Views366Altmetric-Citations120LEARN 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 (4 MB) Get e-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
Triosephosphate isomerase deficiency: a neurodegenerative misfolding disease (2002)

Conference Abstract| February 01 2002 Triosephosphate isomerase deficiency: a neurodegenerative misfolding disease Judit Olah; Judit Olah 1Institute of Enzymology, Hungarian Academy of Sciences, Budapest, H-1518, P.O.Box 7, Hungary Search for other works by this author on: This Site PubMed Google Scholar Ferenc Orosz; Ferenc Orosz 1Institute of Enzymology, Hungarian Academy of Sciences, Budapest, H-1518, P.O.Box 7, Hungary Search for other works by this author on: This Site PubMed Google Scholar Gyorgy Keseru; Gyorgy Keseru 2Chemical Works of Gedeon Richter Ltd., Budapest Search for other works by this author on: This Site PubMed Google Scholar Janos Kovacs; Janos Kovacs 3Department of General Zoology, University of Eotvos Lorand, Budapest Search for other works by this author on: This Site PubMed Google Scholar Susan Hollan; Susan Hollan 4National Institute of Blood Transfusion, Budapest Search for other works by this author on: This Site PubMed Google Scholar Judit Ovadi Judit Ovadi 1Institute of Enzymology, Hungarian Academy of Sciences, Budapest, H-1518, P.O.Box 7, Hungary Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (2002) 30 (1): A6. https://doi.org/10.1042/bst030a006a Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter LinkedIn Cite Icon Cite Get Permissions Citation Judit Olah, Ferenc Orosz, Gyorgy Keseru, Janos Kovacs, Susan Hollan, Judit Ovadi; Triosephosphate isomerase deficiency: a neurodegenerative misfolding disease. Biochem Soc Trans 1 February 2002; 30 (1): A6. doi: https://doi.org/10.1042/bst030a006a Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu nav search search input Search input auto suggest search filter All ContentAll JournalsBiochemical Society Transactions Search Advanced Search This content is only available as a PDF. © 2002 Biochemical Society2002 Article PDF first page preview Close Modal You do not currently have access to this content.
An increased bone mineral density is an adverse prognostic factor in patients with systemic mastocytosis (2020)

Osteoporosis is a common feature in ISM but not in AdvSM. An increased BMD is frequently present in AdvSM but not in ISM and is associated with more advanced disease and inferior outcome.
Angular momentum fluctuations of the ideal Bose gas in a rotating bucket (1995)

An equilibrium superfluid is usually modelled by a Bose gas below its transition temperature. Here, we compute rigorously the extremal equilibrium states below this transition temperature. We compute the deviation from normality of the angular momentum fluctuations both above and below this transition temperature. Finally, we compute the distribution functions of the angular momentum and its fluctuations.
Basal Activity of a PARP1-NuA4 Complex Varies Dramatically across Cancer Cell Lines (2014)

Poly(ADP-ribose) polymerases (PARPs) catalyze poly(ADP-ribose) addition onto proteins, an important posttranslational modification involved in transcription, DNA damage repair, and stem cell identity. Previous studies established the activation of PARP1 in response to DNA damage, but little is known about PARP1 regulation outside of DNA repair. We developed an assay for measuring PARP activity in cell lysates and found that the basal activity of PARP1 was highly variable across breast cancer cell lines, independent of DNA damage. Sucrose gradient fractionation demonstrated that PARP1 existed in at least three biochemically distinct states in both high- and low-activity lines. A discovered complex containing the NuA4 chromatin-remodeling complex and PARP1 was responsible for high basal PARP1 activity, and NuA4 subunits were required for this activity. These findings present a pathway for PARP1 activation and a direct link between PARP1 and chromatin remodeling outside of the DNA damage response.
Enhanced Tim3 Activity Improves Survival after Influenza Infection (2012)

Influenza is a major cause of morbidity and mortality in the United States. Studies have shown that excessive T cell activity can mediate pneumonitis in the setting of influenza infection, and data from the 2009 H1N1 pandemic indicate that critical illness and respiratory failure postinfection were associated with greater infiltration of the lungs with CD8+ T cells. T cell Ig and mucin domain 3 (Tim3) is a negative regulator of Th1/Tc1-type immune responses. Activation of Tim3 on effector T cells has been shown to downregulate proliferation, cell-mediated cytotoxicity, and IFN-γ production, as well as induce apoptosis. In this article, we demonstrate that deletion of the terminal cytoplasmic domain of the Tim3 gene potentiates its ability to downregulate Tc1 inflammation, and that this enhanced Tim3 activity is associated with decreased phosphorylation of the TCR-CD3ζ-chain. We then show that mice with this Tim3 mutation infected with influenza are protected from morbidity and mortality without impairment in viral clearance or functional heterotypic immunity. This protection is associated with decreased CD8+ T cell proliferation and decreased production of inflammatory cytokines, including IFN-γ. Furthermore, the Tim3 mutation was protective against mortality in a CD8+ T cell-specific model of pneumonitis. These data suggest that Tim3 could be targeted to prevent immunopathology during influenza infection and demonstrate a potentially novel signaling mechanism used by Tim3 to downregulate the Tc1 response.
The optical properties of LiNbO3 single crystals obtained in air atmosphere (1999)

Single crystals of LiNbO3 were grown by the Czochralski technique in an air atmosphere. The critical diameter and the critical rate of rotation were calculated. X-Ray measurements of the powder were carried out to obtain the lattice parameters.The optical constants were calculated by Kramers-Kronig analysis of reflectance data. The optical properties of LiNbO3 single crystals were studied for samples grown in an air atmosphere to investigate the influence of air on the optical properties of the formed crystals. A peak due to OH. gtroups appears in the transmission spectrum at 3385 cm -1. It was still present after annealing in an air atmosphere at temperature up to 873 K, but it was no longer detectable after annealing at 1473 K in an electric field. Thick films of the high-temperature superconductor YBa2Cu3O7 (Ag) were obtained on plates of LiNbO3 single crystals. The obtained results are discussed and compared with published data.
SITE-SPECIFIC MODIFICATIONS OF DIVALENT ANTIBODY FRAGMENTS FOR RAID AND RAIT (1994)

s: Fifth Conference on Radioimmunodetection and Radioimmunotherapy of Cancer: Session I: Radiochemistry of Antibodies: PDF Only
Comparison of DNA damage and single- and double-strand breakage activities on PM-2 DNA by talisomycin and bleomycin analogs. (1980)

Single- and double-strand breakage of isolated PM-2 DNA by structural analogs of the glycopeptide antitumor antibiotics bleomycin (BLM) and talisomycin (TLM) was investigated. Breakage of PM-2 DNA was determined by two systems: an ethidium bromide fluorescence assay; and agarose gel electrophoresis. The fluorescence assay, which measures total breakage of DNA including single- and double-strand breakage and alkaline labile damage, showed that the BLM's, A2 and B2 induced more total DNA breakage than did the TLM's A, B, S2b, and S10b. As measured by the comparison of the concentration of analog required to cause 50% breakage of superhelical DNA, BLM's A2 and B2 were 10 times more active than TLM's S2b and S10b and 25 times more active than TLM's A and B. Gel electrophoresis, which measures the extent of both single- and double-strand breakage of DNA, showed that at equivalent levels of breakage of superhelical DNA each of the TLM's caused more double-strand breakage of DNA than did the BLM's. Thus, the structural alterations near the bithiazole in the TLM's, which distinguish them structurally from the BLM's, result in a reduction of the total PM-2 DNA breakage activity and enhanced production of double-strand breaks relative to single-strand breaks by TLM when compared to BLM.
BrainImageR: Spatiotemporal gene set analysis referencing the human brain (2017)

Abstract RATIONALE Neurological molecular analyses such as transcriptomics, epigenetics, and genome-wide association studies must be assessed in the context of the human brain in order to generate biologically meaningful inferences. It is often difficult to access primary human brain tissue; therefore, approximations are made using in vitro modeling or by identifying disease-associated genes from DNA extracted from blood. Gene sets from these studies are then compared to the post-mortem human brain to provide an assessment of the brain region and the developmental time point that a gene set is most closely associated with. However, most analyses of postmortem datasets are achieved by building new computational tools each time in-house, which can cause discrepancies from study to study, indicating that the field is in need of a user-friendly suite of tools to examine spatiotemporal expression with respect to the postmortem brain. Such a tool will be of use to the molecular interrogation of neurological and psychiatric disorders, with direct advantages for the disease-modeling and human genetics communities. RESULTS We have developed brainImageR, an R package that calculates both the spatial and temporal association of a dataset with post-mortem gene expression data from the Allen Brain Atlas. BrainImageR performs a robust analysis of gene set enrichment to identify enriched anatomical regions, provides a global high-resolution visualization of these enrichments across the human brain, and predicts when in developmental time the sample is most closely matched to, a task that has become increasingly important in the field of in vitro neuronal modeling. These functionalities of brainImageR enable a quick and efficient characterization of a given dataset across normal human brain development. AVAILABILITY AND IMPLEMENTATION BrainImageR is released under the Creative Commons CC BY-SA 4.0 license and the source code can be downloaded through github at https://github.com/saralinker/brainImageR . CONTACT gage@salk.edu
Effect of interconnection delay on liquid nitrogen temperature CMOS circuit performance (1987)

In this work, the effect of interconnection delay on the performance of CMOS circuits operated at liquid nitrogen temperature is examined. The interconnect is modeled as a distributed RLC line driven by an optimal configuration of cascaded inverters. Using measured aluminum thin film resistivities, the delay time is predicted as a function of interconnect length at both 300 K and 77 K for typical 0.8 7micro;m CMOS technologies. It is shown that the driver resistance, rather than the interconnect resistance itself, limits performance and the improvement in delay time achieved through low temperature operation is close to a factor of two irrespective of interconnect length.