gebhart/patrepeval huggingface dataset:
Molecular Cloning and Characterization of Two Mouse Peroxisome Proliferator-activated Receptor α (PPARα)-regulated Peroxisomal Acyl-CoA Thioesterases (2004)

Peroxisomes are organelles that function in the beta-oxidation of long- and very long-chain acyl-CoAs, bile acid-CoA intermediates, prostaglandins, leukotrienes, thromboxanes, dicarboxylic fatty acids, pristanic acid, and xenobiotic carboxylic acids. The very long- and long-chain acyl-CoAs are mainly chain-shortened and then transported to mitochondria for further metabolism. We have now identified and characterized two peroxisomal acyl-CoA thioesterases, named PTE-Ia and PTE-Ic, that hydrolyze acyl-CoAs to the free fatty acid and coenzyme A. PTE-Ia and PTE-Ic show 82% sequence identity at the amino acid level, and a putative peroxisomal type 1 targeting signal of -AKL was identified at the carboxyl-terminal end of both proteins. Localization experiments using green fluorescent fusion protein showed PTE-Ia and PTE-Ic to be localized in peroxisomes. Despite their high level of sequence identity, we show that PTE-Ia is mainly active on long-chain acyl-CoAs, whereas PTE-Ic is mainly active on medium-chain acyl-CoAs. Lack of regulation of enzyme activity by free CoASH suggests that PTE-Ia and PTE-Ic regulate intraperoxisomal levels of acyl-CoA, and they may have a function in termination of beta-oxidation of fatty acids of different chain lengths. Tissue expression studies revealed that PTE-Ia is highly expressed in kidney, whereas PTE-Ic is most highly expressed in spleen, brain, testis, and proximal and distal intestine. Both PTE-Ia and PTE-Ic were highly up-regulated in mouse liver by treatment with the peroxisome proliferator WY-14,643 and by fasting in a peroxisome proliferator-activated receptor alpha-dependent manner. These data show that PTE-Ia and PTE-Ic have different functions based on different substrate specificities and tissue expression.
Synthesis of Composite Films (1998)

A new method for synthesis of composite films was developed and used to synthesize ZnO—SiO2 and Cu—SiO2 composite films where the silica particle size was varied from 40 nm to 520 nm. The process consists of sequential deposition of particles and the matrix material (using chemical vapor deposition) and can be used for any material system. The morphology of the composite films can be controlled and varied from dense to porous and laminated structures can be formed. The film formation process can be explained in terms of the Thiele modulus. In order to obtain dense films the Thiele modulus for such systems should be < 0.4. For Thiele modulus greater than 0.5 but less than 1.5, the process results in porous films. No infiltration is possible for Thiele modulus > 1.5.
Potential CD8+ T Cell Cross-Reactivity Against SARS-CoV-2 Conferred by Other Coronavirus Strains (2020)

While individuals infected with coronavirus disease 2019 (COVID-19) manifested a broad range in susceptibility and severity to the disease, the pre-existing immune memory to related pathogens cross-reactive against SARS-CoV-2 can influence the disease outcome in COVID-19. Here, we investigated the potential extent of T cell cross-reactivity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that can be conferred by other coronaviruses and influenza virus, and generated an <i>in silico</i> map of public and private CD8+ T cell epitopes between coronaviruses. We observed 794 predicted SARS-CoV-2 epitopes of which 52% were private and 48% were public. Ninety-nine percent of the public epitopes were shared with SARS-CoV and 5.4% were shared with either one of four common coronaviruses, 229E, HKU1, NL63, and OC43. Moreover, to assess the potential risk of self-reactivity and/or diminished T cell response for peptides identical or highly similar to the host, we identified predicted epitopes with high sequence similarity with human proteome. Lastly, we compared predicted epitopes from coronaviruses with epitopes from influenza virus deposited in IEDB, and found only a small number of peptides with limited potential for cross-reactivity between the two virus families. We believe our comprehensive <i>in silico</i> profile of private and public epitopes across coronaviruses would facilitate design of vaccines, and provide insights into the presence of pre-existing coronavirus-specific memory CD8+ T cells that may influence immune responses against SARS-CoV-2.
Peak-to-average power ratio reduction of an OFDM signal using data permutation with embedded side information (2001)

The use of a set of fixed permutations has recently been proposed for peak-to-average power ratio (PAR) reduction of an OFDM signal. Sending the identity of the used permutation to the receiver reliably is critical in this method. This paper presents the use of data permutation with embedded side information (SI) to reduce the PAR of an OFDM signal. SI is coded using a simple forward-error-correction code and inserted into the information sequence. The PARs of the permuted sequences and the original information sequence are then computed using IDFTs. The sequence with the lowest PAR is chosen for the transmission. The PAR statistics do not degrade due to the inclusion of SI. This paper also presents theoretical expressions for the complementary cumulative density function (CCDF) of the PAR of an interleaved OFDM (IOFDM) signal and for the average number of interleavers in the adaptive interleaving approach.
HITlights: A career perspective on heparin‐induced thrombocytopenia (2012)

Two decades of research into heparin-induced thrombocytopenia (HIT) permit a personal historical perspective on this fascinating syndrome. Previously, the frequency of HIT was unknown, although complicating thrombosis was believed to be rare and primarily arterial. The opportunity to apply a remarkable test for "HIT antibodies"--the (14) C-serotonin-release assay (SRA)--to serial plasma samples obtained during a clinical trial of heparin thromboprophylaxis, provided insights into the peculiar nature of HIT, such as, its prothrombotic nature--including its strong association with venous thrombosis (RR = 11.6 [95%CI, 6.4-20.8; P < 0.0001); its more frequent occurrence with unfractionated versus low-molecular-weight heparin; the "iceberg" model, which states that among the many patients who form anti-PF4/heparin antibodies during heparin therapy, only a minority whose antibodies evince strong platelet-activating properties develop HIT; and the characteristic HIT timeline, whereby serum/plasma antibodies are readily detectable at or prior to the HIT-associated platelet count fall. Applying the SRA also to patients encountered in clinical practice led to recognition of warfarin-induced venous limb gangrene (for which HIT is a major risk factor via its extreme hypercoagulability) and delayed-onset HIT (whereby thrombocytopenia begins or worsens following heparin discontinuation, due to the ability of HIT antibodies strongly to activate platelets even in the absence of heparin--so-called heparin-"independent" platelet activation). Recent concepts include the increasing recognition of HIT "overdiagnosis" (due to the low diagnostic specificity of the widely-applied PF4-dependent immunoassays), and the observation that HIT-associated consumptive coagulopathy is a risk factor for treatment failure with PTT-adjusted direct thrombin inhibitor therapy ("PTT confounding" secondary to HIT-associated coagulopathy).
New optical technique for measuring erythrocyte deformability with the ektacytometer. (1980)

The laser light scattered by erythrocytes subjected to a well-defined shear stess can be analyzed with the ektacytometer to obtain information regarding the changes in cell shape due to fluid shear. We describe an optical technique whereby an observed quantitative output derived from a mesurement of light intensity through a spatial filter is related to the change in cellular dimensions that were previously observed under similar fluid-shear conditions by use of microscopy and a cone-plate viscometer (rheoscope). We also present the predictions of a theoretical model (of the ektacytometer) based on approximations of light-scattering theory developed for nonspherical particles, and give preliminary results for the accuracy and sensitivity of this measurement of erythrocyte deformability. With this optical technique the instrumentation (ektacytometer) is made quite simple and suitable for use in the typical laboratory. This would allow a regular, quantitative assessment of this important blood cell quality, to supplement the data obtained from the complete blood count.
ONYX-015 works synergistically with chemotherapy in lung cancer cell lines and primary cultures freshly made from lung cancer patients. (2000)

p53 mutations and loss of heterozygosity (LOH) have been detected in >50% of lung cancers. Wild-type p53 can prevent replication of damaged DNA and promote apoptosis of cells with abnormal DNA. A human adenovirus, ONYX-015, which has a deletion in the E1B region, has shown tumor-specific cytolytic effect in tumor cells with nonfunctional p53 and antitumor efficacy that can be augmented by chemotherapeutic agents. A recent report from an independent group, however, indicates that wild-type p53 is necessary for the infection of this replicating virus, and it is in direct contradiction to previous observations of the ONYX group. In this study, we carried out cytopathic effect (CPE) assays using ONYX-015 on five human lung cancer cell lines with known p53 status. Two of these cell lines, NCI-H522 and NCI-H1703, have mutations and LOH in their p53 gene. Both lines were lysed in a dose-dependent manner and showed 100% cytolysis at a multiplicity of infection of 0.1. Two additional cell lines, NCI-H2347 and NCI-H838, both of which have wild-type p53 gene, showed near complete lysis at a multiplicity of infection of 1. We demonstrate here that the lung cancer cells with nonfunctional p53 are at least 10 times more sensitive to ONYX-015 cytolysis than the lung cancer cells with wild-type p53. In addition, standard chemotherapeutic agents (paclitaxol and cisplatin) showed a synergistic effect when combined with ONYX-015, and this effect was p53 mutant dependent. Furthermore, we tested the cytolytic effect of ONYX-015 on a panel (n = 7) of primary first-passage cultures made from freshly resected lung cancers. ONYX-015 lysed primary lung cancer cells in six of seven (86 %) primary cultures. Two of four primary cultures treated with chemotherapeutic agents had a synergistic effect with ONYX-015. Our data indicate that wild-type p53 is not required for the infection of this replicating virus, and also we demonstrate that ONYX-015 is effective alone and works synergistically with chemotherapeutic agents in lung cancer cell lines and primary cultures. This study suggests that ONYX-015 may be effective, especially in combination with conventional chemotherapy, in the treatment of patients with lung cancer.
Charge transport in PbSe nanocrystal arrays (2008)

We report electrical transport measurements of arrays of PbSe nanocrystals forming the channels of field-effect transistors. We measure the current in these devices as a function of source-drain voltage, gate voltage, and temperature. Annealing is necessary to observe measurable current, after which a simple model of hopping between intrinsic localized states describes the transport properties of the nanocrystal solid. We find that the majority carriers are holes, which are thermally released from acceptor states. At low source-drain voltages, the activation energy for the conductivity is given by the energy required to generate holes plus the activation over barriers resulting from site disorder. At high source-drain voltages, the activation energy is given by the former only. The thermal activation energy of the zero-bias conductance indicates that the Fermi energy is close to the highest-occupied valence level, the $1{S}_{h}$ state, and this is confirmed by field-effect measurements, which give a density of states of approximately 8 per nanocrystal as expected from the degeneracy of the $1{S}_{h}$ state.
Effects of clozapine and other dibenzo-epines on central dopaminergic and cholinergic systems. Structure-activity relationships. (1977)

Structure-activity relationships of 16 dibenzoepines, including clozapine, loxapine, clothiapine and perlapine, have been investigated with regard to locomotor inhibition, cataleptogenesis, apomorphine antagonism, arousal inhibition, effect on striatal dopamine metabolism, and in vivo and in vitro anticholinergic potency. Thioridazine and the classical neuroleptics haloperidol and chlorpromazine were included in the study for comparison. The classical tests used to detect neuroleptic activity in laboratory animals were found to be poor predictors of possible clinical effectiveness of the dibenzo-epines.
Acquisition of resistance to antifolates caused by enhanced gamma-glutamyl hydrolase activity. (1993)

A subline of H35 hepatoma cells has been developed which exhibits 80-fold resistance to 5,10-dideazatetrahydrofolate, an antifolate which inhibits glycinamideribonucleotide transformylase. The cells are cross-resistant to methotrexate, an inhibitor of dihydrofolate reductase and 10-propargyl-5,8-dideazafolate and its 2-desamino-2-methyl derivative, both inhibitors of thymidylate synthase. The resistant cells are characterized by an impaired activity of the reduced folate transport system which affects cellular import of methotrexate, 5,10-dideazatetrahydrofolate, and 2-desamino-2-methyl-10-propargyl-5,8-dideazafolate but not 10-propargyl-5,8-dideazafolate. In addition, the resistant cells exhibit a severalfold increased activity of gamma-glutamyl hydrolase, the enzyme which cleaves the intracellular polyglutamate derivatives of the antifolates. Evidence for the involvement of gamma-glutamyl hydrolase in resistance is derived from the observation that polyglutamate derivatives of 10-propargyl-5,8-dideazafolate in resistant cells are maintained at one-third the amount of that in parental cells in the presence of the same extracellular concentration. This is the first observation that an increase in gamma-glutamyl hydrolase contributes to acquired resistance to antifolates.
Production and Level of Genetic Stability of an Influenza A Virus Temperature-Sensitive Mutant Containing Two Genes with ts Mutations (1982)

Temperature-sensitive (ts) reassortant vaccine strains derived from the A/Udorn/72 ts-1A2 donor virus were not sufficiently stable genetically in humans. We therefore sought to produce a new, more stable donor virus. We had previously identified a stable ts virus with a ts P3 gene and in the current study identified another relatively stable single-lesion ts virus with a ts mutation in the NP gene. A new ts reassortant virus was constructed by mating these two single mutants and by isolating three reassortant progeny, clones 20, 53, and 55, that contained both a ts P3 and a ts NP gene. These reassortant progeny possessed a 37 to 38 degrees C shutoff temperature and were as restricted in their replication in hamster lungs as the A/Udorn/72 ts-1A2 virus. All isolates from the lungs and nasal turbinates of hamsters were temperature sensitive. An in vitro stress test was used to determine whether the new ts P3 ts NP reassortant virus would undergo loss of its ts phenotype after replication at semipermissive temperature. Clone 20 and 55 reassortants underwent progressive loss of their ts phenotype in vitro, although at a rate slightly less than that of the A/Udorn/72 ts-1A2 virus. The level of genetic stability after replication in vivo was assessed in cyclophosphamide-treated hamsters in which virus replication continued for up to 15 days. Again, both the A/Udorn/72 ts-1A2 and the new ts P3 ts NP reassortant clone 55 manifested a progressive loss of temperature sensitivity after 7 days of replication. Clone 55 virus lost temperature sensitivity significantly less rapidly than the A/Udorn/72 ts-1A2 virus. These results indicated that, although the new ts P3 ts NP reassortant virus was more stable than the A/Udorn/72 ts-1A2 virus, it nevertheless underwent progressive loss of temperature sensitivity after replication in vitro and in vivo. Therefore, it does not appear to be a satisfactory donor virus. This experience plus that gained earlier with other ts mutants of influenza A virus suggest that influenza A virus mutants that rely solely upon their ts phenotype for attenuation are unlikely to exhibit the phenotypic stability required of a vaccine virus. Other genetic techniques are needed to produce more stable influenza A virus strains.
The effect of the heat of association on homogeneous nucleation rates in methanol vapor (1986)

Homogeneous nucleation rates in methanol vapor were measured using the expansion pulse technique. Our results show an apparently inverted temperature dependence. The obtained data are consistent with earlier expansion chamber investigations, reported in the literature, however, strong deviations from corresponding diffusion chamber data are observed. In the present paper we show that these deviations can be explained by considering vapor association during adiabatic expansion. The homogeneous nucleation rates are found to be drastically reduced due to the latent heat released during the formation of subcritical clusters. Thereby the severe discrepancies between expansion chamber experiments for methanol and the corresponding diffusion chamber data are now essentially resolved. Furthermore, an apparently anomalous behavior of ethanol vapor, observed in expansion chambers at higher temperatures, is now qualitatively understood.
Comparative design review (1993)

Three user interface designers were asked to design interfaces for a given problem. These designs were made available to a group of usability specialists for heuristic evaluation. The reviewers will lead off the panel with specific questions to the designers regarding the usability aspects of their designs. The panel will feature a lively discussion of the designers' various approaches and solutions.
Glycosyltransferase mutants: key to new insights in glycobiology (1995)

Glycosyltransferases (Glyc-T's) catalyze the synthesis of the carbohydrate portions of glycoproteins, glycolipids, and proteoglycans. Most Glyc-T's transfer one sugar in one linkage and are encoded by a unique gene. Thus, synthesis of a branched carbohydrate may require expression of at least 30 Glyc-T genes. Mutations that alter Glyc-T activity therefore provide an approach to identifying functions for carbohydrates. These fall into two general categories: 1) intramolecular functions pertaining to the physical and biochemical properties of a glycoconjugate; and 2) intermolecular functions that involve recognition of sugar (or sugars) by another molecule, such as the selectins that bind to specific sugar sequences at the cell surface. In this review, the origin, nature, and uses of Glyc-T mutants that have been used to study both types of carbohydrate function will be summarized. Many Glyc-T genes are now cloned, so transgenic and gene disruption techniques are the latest strategies for identifying new functions for carbohydrates. It is already apparent that the consequences of altering the spectrum of carbohydrates expressed by a cell or an organism range from "none" to "death." A key challenge for the future is to identify molecular bases for the complex phenotypes created by glycosylation engineering. Equally important will be to understand factors that regulate Glyc-T genes, a new class of genes whose study may reveal novel mechanisms of biological regulation.
A multi-beam x-ray imaging system based on carbon nanotube field emitters (2006)

In this study, we report a multi-beam x-ray imaging system that can generate a scanning x-ray beam to image an object from multiple projection angles without mechanical motion. The key part of this imaging system is a multi-beam field emission x-ray (MBFEX) source which comprises a linear array of gated electron emitting pixels. The pixels are individually addressable via a MOSFET (metal-oxide-semiconductor field effect transistor) based electronic circuit. The device can provide a tube current of 0.1-1 mA at 40 kVp with less than 300 &mu;m focal spot size from each of the emitting pixels. Multilayer images of different phantoms were reconstructed to demonstrate its potential applications in tomographic imaging. Since no mechanical motion is needed and the electronic switching time is generally negligible the MBFEX system has the potential to simplify the system design and lead to a fast data acquisition for tomographic imaging.
Extracellular Accumulation of the Polyol Lipids, 3,5-Dihydroxydecanoyl and 5-Hydroxy-2-decenoyl Esters of Arabitol and Mannitol, byAureobasidiumsp. (1994)

Many isolated strains of Aureobasidium sp. were found to produce extracellular lipids as heavy oils in culture media containing no CaCO3 as a neutralizing agent. The lipids (35 g) were recovered from the culture broth (1 liter) of a light-colored mutant of Aureobasidium sp. A-2 and proved to be a mixture of fatty acid esters of arabitol and mannitol. The two main components of the lipophilic moiety of the lipids proved to be 3,5-dihydroxydecanoic and 5-hydroxy-2-decenoic acids by the identification of their lactones, (+)-3-hydroxydecan-5-olide and (R)-(−)-2-decen-5-olide, that is, R-(−)-massoilactone, respectively.
Over‐expression of TGA5, which encodes a bZIP transcription factor that interacts with NIM1/NPR1, confers SAR‐independent resistance in Arabidopsis thaliana to Peronospora parasitica (2002)

The Arabidopsis thaliana NIM1/NPR1 gene product is required for induction of systemic acquired resistance (SAR) by pathogens, salicylic acid (SA) or synthetic SA analogs. We identified, in a yeast two-hybrid screen, two NIM1/NPR1 interacting proteins, TGA2 and TGA5, which belong to the basic region, leucine zipper (bZIP) family of transcription factors. Both TGA2 and TGA5 strongly interact with NIM1/NPR1 in yeast and in vitro, and recognize the as-1 cis element found within the promoter of several pathogenesis-related genes, such as PR-1. To determine the role TGA2 and TGA5 may play in NIM1/NPR1-mediated disease resistance, we introduced sense and antisense versions of both genes into transgenic Arabidopsis plants. Characterization of TGA2 transgenic plants revealed that inhibition or overexpression of TGA2 does not significantly affect PR-1 expression or induction of SAR after pathogen infection or INA treatment. Surprisingly, all TGA5-antisense transgenic plants produced showed increased accumulation of TGA5 transcripts compared with untransformed control plants, while the TGA5-sense lines showed no significant increase in TGA5 mRNA levels. Interestingly, the high level of TGA5 mRNA in the antisense lines was accompanied by significant resistance to a highly virulent isolate of the oomycete pathogen Peronospora parasitica. Further, resistance was not coupled to accumulation of products from the SAR-linked PR-1 gene following inoculation with P. parasitica or treatment with INA, indicating that these plants express a robust, PR-1-independent resistance mechanism. Resistance was retained when a TGA5-accumulating line was combined genetically with a nim1-1 mutation or nahG (salicylate hydroxylase) transgene, indicating that resistance in these plants is due to an SA and SAR-independent mechanism.