gebhart/patrepeval huggingface dataset:
An efficient CPLD technology mapping under the time constraint (2002)

In this paper, we proposed a new technology mapping algorithm for CPLD under a time constraint (TMCPLD). In our technology mapping algorithm, a given Boolean network generated a feasible cluster. The generated feasible cluster creates clusters with minimum area under the time constraint. A covered Boolean network is transformed to a Boolean equation. The transformed equations are reconstructed in order to fit the architecture of a selected target CPLD using collapsing and bin-packing. To demonstrate the efficiency of our approach, we applied our algorithm to MCNC benchmarks and compared the results with those of the existing algorithms. The experimental results show that our approach is better than any of the existing algorithms in the number of logic blocks.
Apolipoprotein J Is Associated with Paraoxonase in Human Plasma (1994)

Apolipoprotein J (apoJ)-containing high-density lipoproteins (HDL), isolated from human plasma by immunoaffinity chromatography, are associated with apoAI and a protein of approximately 44 kDa. In order to advance our understanding of apoJ's role in the vasculature, a comprehensive investigation was performed to identify and characterize this 44-kDa protein and to study its interaction with apoJ. The 44-kDa protein, a monomeric glycoyslated polypeptide, was identified by N-terminal sequencing as serum paraoxonase. Paraoxonase exists in two oxidation states: one contains all free cysteines while the other has one disulfide bond between Cys42 and Cys284. Northern analysis of eight human tissues shows paraoxonase message present only in the liver. The majority of apoJ/paraoxonase-HDL are 90-140 kDa; however, not all of the plasma paraoxonase is associated with apoJ. The specificity of the apoJ/paraoxonase interaction, inferred by the constant mole ratio of the two proteins in affinity-purified apoJ-HDL, is confirmed in direct binding assays. For purified proteins, there is more than a 5-fold increase in the apparent affinity of apoJ for immobilized paraoxonase as the paraoxonase coating concentration is increased from 0.5 to 2.0 micrograms/mL. Both oxidation states of paraoxonase bind to apoJ with equal affinity. Our data combined with other evidence suggest that the plasma link of apoJ with paraoxonase will be implicated as a predictor of vascular damage.
Blockade of the Activin Receptor IIB Activates Functional Brown Adipogenesis and Thermogenesis by Inducing Mitochondrial Oxidative Metabolism (2012)

Brown adipose tissue (BAT) is a key tissue for energy expenditure via fat and glucose oxidation for thermogenesis. In this study, we demonstrate that the myostatin/activin receptor IIB (ActRIIB) pathway, which serves as an important negative regulator of muscle growth, is also a negative regulator of brown adipocyte differentiation. In parallel to the anticipated hypertrophy of skeletal muscle, the pharmacological inhibition of ActRIIB in mice, using a neutralizing antibody, increases the amount of BAT without directly affecting white adipose tissue. Mechanistically, inhibition of ActRIIB inhibits Smad3 signaling and activates the expression of myoglobin and PGC-1 coregulators in brown adipocytes. Consequently, ActRIIB blockade in brown adipose tissue enhances mitochondrial function and uncoupled respiration, translating into beneficial functional consequences, including enhanced cold tolerance and increased energy expenditure. Importantly, ActRIIB inhibition enhanced energy expenditure only at ambient temperature or in the cold and not at thermoneutrality, where nonshivering thermogenesis is minimal, strongly suggesting that brown fat activation plays a prominent role in the metabolic actions of ActRIIB inhibition.
Trehalase Deficiency (1982)

Perspectives in nutrition suggest a greater use of single-cell proteins in the future. The problems of a high purine content and of potential allergens have been solved by technology. The single-cell proteins may contain trehalose, the absorption of which by the human intestine necessitates prior hydrolysis by trehalase, a specific brush-border disaccharidase. The enzymatic analysis of 100 intestinal biopsies discovered 2 cases of very low trehalase level, with an expected clinical intolerance to even small doses of trehalose. It is concluded that tolerance to high doses of trehalose should be excellent in about 98% of healthy people.
The Google file system (2003)

article Share on The Google file system Authors: Sanjay Ghemawat Google GoogleView Profile , Howard Gobioff Google GoogleView Profile , Shun-Tak Leung Google GoogleView Profile Authors Info & Claims ACM SIGOPS Operating Systems ReviewVolume 37Issue 5December 2003 pp 29–43https://doi.org/10.1145/1165389.945450Online:19 October 2003Publication History 2,942citation59,825DownloadsMetricsTotal Citations2,942Total Downloads59,825Last 12 Months2,935Last 6 weeks416 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Mitochondrial theory of aging matures--roles of mtDNA mutation and oxidative stress in human aging. (2001)

Mitochondrial theory of aging, a variant of free radical theory of aging, proposes that accumulation of damage to mitochondria and mitochondrial DNA (mtDNA) leads to aging of humans and animals. It has been supported by the observation that mitochondrial function declines and mtDNA mutation increases in tissue cells in an age-dependent manner. Age-related impairment in the respiratory enzymes not only decreases ATP synthesis but also enhances production of reactive oxygen species (ROS) through increased electron leakage in the respiratory chain. Human mtDNA, which is not protected by histones and yet is exposed to high levels of ROS and free radicals in the matrix of mitochondria, is susceptible to oxidative damage and mutation in tissue cells. In the past decade, more than one hundred mtDNA mutations have been found in patients with mitochondrial disease, and some of them also occur in aging human tissues. The incidence and abundance of these mutant mtDNAs are increased with age, particularly in tissues with great demand for energy. On the other hand, recent studies have revealed that the ability of the human cell to cope with oxidative stress is compromised in aging. Comparative analysis of gene expression by microarray technology has shown that a number of genes related to oxidative stress response are altered in aging animals. We discovered that the transcripts of early growth response protein-1, growth arrest and DNA damage-inducible proteins and glutathione S-transferase genes are increased in response to oxidative stress in human skin fibroblasts. Moreover, the activities of Cu,Zn-SOD, catalase and glutathione peroxidase decrease with age, whereas Mn-SOD activity increases with age up to 65 years and slightly declines thereafter in skin fibroblasts. Such an imbalance in the function of antioxidant enzymes may result in excess production of damaging ROS in the cell. This notion is supported by the observation that intracellular levels of H2O2 and oxidative damage to DNA and lipids are significantly increased with age of the fibroblast donor. Furthermore, the mitochondrial pool of reduced glutathione declines and DNA damage is enhanced in aging tissues. Taken together, these observations and our previous findings that mtDNA mutations and oxidative damage are increased in aging human tissues suggest that mitochondrial theory of aging is mature.
A c-Myc–SIRT1 feedback loop regulates cell growth and transformation (2009)

The protein deacetylase SIRT1 has been implicated in a variety of cellular functions, including development, cellular stress responses, and metabolism. Increasing evidence suggests that similar to its counterpart, Sir2, in yeast, Caenorhabditis elegans, and Drosophila melanogaster, SIRT1 may function to regulate life span in mammals. However, SIRT1's role in cancer is unclear. During our investigation of SIRT1, we found that c-Myc binds to the SIRT1 promoter and induces SIRT1 expression. However, SIRT1 interacts with and deacetylates c-Myc, resulting in decreased c-Myc stability. As a consequence, c-Myc's transformational capability is compromised in the presence of SIRT1. Overall, our experiments identify a c-Myc-SIRT1 feedback loop in the regulation of c-Myc activity and cellular transformation, supporting/suggesting a role of SIRT1 in tumor suppression.
Characterization of the Magnitude and Kinetics of Xanthine Oxidase-catalyzed Nitrite Reduction (2001)

Xanthine oxidase (XO)-catalyzed nitrite reduction with nitric oxide (NO) production has been reported to occur under anaerobic conditions, but questions remain regarding the magnitude, kinetics, and biological importance of this process. To characterize this mechanism and its quantitative importance in biological systems, electron paramagnetic resonance spectroscopy, chemiluminescence NO analyzer, and NO electrode studies were performed. The XO reducing substrates xanthine, NADH, and 2,3-dihydroxybenz-aldehyde triggered nitrite reduction to NO, and the molybdenum-binding XO inhibitor oxypurinol inhibited this NO formation, indicating that nitrite reduction occurs at the molybdenum site. However, at higher xanthine concentrations, partial inhibition was seen, suggesting the formation of a substrate-bound reduced enzyme complex with xanthine blocking the molybdenum site. Studies of the pH dependence of NO formation indicated that XO-mediated nitrite reduction occurred via an acid-catalyzed mechanism. Nitrite and reducing substrate concentrations were important regulators of XO-catalyzed NO generation. The substrate dependence of anaerobic XO-catalyzed nitrite reduction followed Michaelis-Menten kinetics, enabling prediction of the magnitude of NO formation and delineation of the quantitative importance of this process in biological systems. It was determined that under conditions occurring during no-flow ischemia, myocardial XO and nitrite levels are sufficient to generate NO levels comparable to those produced from nitric oxide synthase. Thus, XO-catalyzed nitrite reduction can be an important source of NO generation under ischemic conditions.
Making Better Chimeric Antigen Receptors for Adoptive T-cell Therapy (2016)

Chimeric antigen receptors (CAR) are engineered fusion proteins constructed from antigen recognition, signaling, and costimulatory domains that can be expressed in cytotoxic T cells with the purpose of reprograming the T cells to specifically target tumor cells. CAR T-cell therapy uses gene transfer technology to reprogram a patient's own T cells to stably express CARs, thereby combining the specificity of an antibody with the potent cytotoxic and memory functions of a T cell. In early-phase clinical trials, CAR T cells targeting CD19 have resulted in sustained complete responses within a population of otherwise refractory patients with B-cell malignancies and, more specifically, have shown complete response rates of approximately 90% in patients with relapsed or refractory acute lymphoblastic leukemia. Given this clinical efficacy, preclinical development of CAR T-cell therapy for a number of cancer indications has been actively investigated, and the future of the CAR T-cell field is extensive and dynamic. Several approaches to increase the feasibility and safety of CAR T cells are currently being explored, including investigation into the mechanisms regulating the persistence of CAR T cells. In addition, numerous early-phase clinical trials are now investigating CAR T-cell therapy beyond targeting CD19, especially in solid tumors. Trials investigating combinations of CAR T cells with immune checkpoint blockade therapies are now beginning and results are eagerly awaited. This review evaluates several of the ongoing and future directions of CAR T-cell therapy.
Comparative biodistributions of yttrium- and indium-labeled monoclonal antibody B72.3 in athymic mice bearing human colon carcinoma xenografts. (1989)

The biodistribution of yttrium- and indium-labeled monoclonal antibody (MAb) B72.3 IgG using three different chelate conjugates (SCN-Bz-EDTA, CA-DTPA, and SCN-Bz-DTPA) was compared in athymic mice bearing LS-174T tumors. The 88Y-SCN-Bz-DTPA-B72.3 yielded 40% ID/g at 5-7 days in the tumors, while the 88Y-SCN-Bz-EDTA-B72.3 and 88Y-CA-DTPA-B72.3 showed only 6-8% ID/g. The yttrium uptake in the bone with the SCN-Bz-EDTA and CA-DTPA conjugated IgG was over 14 and 11% ID/g, respectively, while 88Y-SCN-Bz-DTPA-B72.3 showed only 3% ID/g. In contrast, the 111In-labeled B72.3 uptake in the bone with all three chelate conjugates was 2-3% ID/g. The differences in yttrium- versus indium-labeled MAb biodistributions demonstrate the difficulty in using 111In-labeled MAbs to predict the biodistribution and dosimetry of 90Y-labeled MAbs unless chelate conjugates such as SCN-Bz-DTPA are used.
Analysis of Stimulants in Oral Fluid and Urine by Gas Chromatography-Mass Spectrometry II: Pseudophedrine (2010)

This study was designed to optimize a method for the identification and quantification of ephedrines in oral fluid (OF) and for its application to subjects taking different doses of pseudoephedrine. Ephedrines use by athletes is banned by World Anti-Doping Agency (WADA), only "in competition" if their concentration in urine exceeds the cutoff limit. The study aimed to establish if there is a correlation in terms of times of elimination and of concentration trends of ephedrine in OF and urine after administration of therapeutic doses of pseudoephedrine to various subjects. Results obtained from excretion studies performed on eight subjects showed reproducible times of disappearance of ephedrines from OF. Pseudoephedrine was generally at low concentrations or undetectable in oral fluid samples 12 h after administration, whereas urine samples collected in the same period of time showed higher ephedrine concentrations and exceeding cutoff values generally between 8 and 24 h after administration of the drug. Within- and between-individual variability was observed in terms of concentrations of pseudoephedrine in OF following the administration of the same dose. Only in the case of sustained-release drugs were constant pseudoephedrine concentrations achieved in OF.
EGF and TGF‐alpha are potent chemoattractants for endothelial cells and EGF‐like peptides are present at sites of tissue regeneration (1989)

We report here that epidermal growth factor (EGF) isolated from male mouse salivary glands is active as a potent chemoattractant for a rat heart vascular endothelial cell line (RHEC). Human EGF and transforming growth factor-alpha (TGF-alpha) produced in Escherichia coli are also active as chemoattractants for these cells. The chemotactic response of the cells is induced by concentrations of murine EGF that ranged from 0.01 to 1.0 nM with similar specific activities for both the human EGF and TGF-alpha. Other growth factors such as fibroblast growth factor (FGF), TGF-beta, platelet-derived growth factor (PDGF), insulin, or IGF were not active as chemoattractants for these cells. The chemotactic response exhibited similar kinetics to those reported for connective tissue cells responding to PDGF (2-6 h) and required both RNA and protein synthesis. However, in contrast to NIH/3T3 cells responding to PDGF, the proliferating cultures of RHEC respond as well as growth-arrested cultures in the chemotaxis assay. In in vivo studies of connective tissue regeneration it appears that EGF-like factors are present in wound fluid collected from rats. Acid extracts of wound fluid contained a RHEC chemotactic activity that was neutralized with anti-EGF antisera. These studies indicate that EGF-like factors may function in vivo to control in part the angiogenic events that occur during tissue repair.
Factor V Level Affects the Host Susceptibility to Group A Streptococcal Infection. (2005)

Abstract Group A streptococci (GAS), a common human pathogen, secrete streptokinase (SK), which activates the host’s plasminogen (PLG). SK is highly specific for human PLG, exhibiting little or no activity against other mammalian species. We demonstrated the major role of the PLG/SK interaction in GAS pathogenicity using a transgenic murine model expressing human plasminogen with increased susceptibility to human pathogenic streptococci. We hypothesize that GAS hijack the host fibrinolytic system in order to circumvent local thrombosis for systemic spread. Markedly increased mortality was also observed following GAS injection in C57BL/6J mice treated with the snake venom Ancrod, which proteolytically degrades plasma fibrinogen, supporting the critical roles of coagulation in host/pathogen interaction. However, fibrinogen also plays important roles in inflammation and immune response, it is necessary to use independent genetic models to further test the impact of coagulation in host defense against bacterial infection. The effect of variations in FV on mouse susceptibility to streptococcal infection was tested. We established a mouse model with low plasma FV level. These mice have a slightly increased bleeding time, though otherwise phenotypically normal. Subjected to streptococcal infection, these mice exhibited significantly increased mortality than wildtype controls, suggesting that the decreased thrombotic tendency in the low FV mice increases host susceptibility to infection. FV Leiden is a common prothrombotic mutation among Caucasian population with an incidence between 4% and 6%. Previous studies from Kerlin et al demonstrated the FV Leiden conferred survival advantage in patients with severe sepsis and in mice challenged with endotoxin. This may be an example of balanced gene polymorphism that maintains the FV Leiden mutant in the general gene pool by selection of bacterial infections. In order to identify the selective agents responsible for the prevalence of FV Leiden mutation, we took advantage of our plasminogen transgenic murine model for streptococcal infection to test whether streptococci is one of the selective agents. Human plasminogen transgene was introduced into FV Leiden background and the susceptibility to streptococcal infection was measured. No significant improvement of survival was observed in the FV Leiden mouse comparing with the wildtype control. Thus, streptococcal infection is not the selective agent for the prevalence of FV Leiden mutation. These observations highlight the potential role of variations in blood coagulation factors in host susceptibility to bacterial infection.
Stream Control Transmission Protocol (2022)

This document describes the Stream Control Transmission Protocol (SCTP). SCTP is designed to transport PSTN signaling messages over IP networks, but is capable of broader applications.
Lubricin reduces cartilage--cartilage integration. (2004)

Cartilage integration in vivo does not occur, such that even cartilage fissures do not heal. This could be due not only to the limited access of chondrocytes to the wound, but also to exogenous factors. In this paper, we tested the hypothesis that lubricin, a lubricating protein physiologically present in the synovial fluid, reduces the integrative cartilage repair capacity. Disk/ring composites of bovine articular cartilage were prepared using concentric circular blades and cultured for 6 weeks with or without treatment with 250 microg/ml lubricin applied three times per week. Following culture, the percentage of contact area between the disks and the rings, as assessed by light microscopy, were equal in both groups. The adhesive strength of the integration interface, as assessed by push-out mechanical tests, was markedly and significantly lower in lubricin-treated specimens (2.5 kPa) than in the controls (28.7 kPa). Histological observation of Safranin-O stained cross-sections confirmed the reduced integration in the lubricin treated composites. Our findings suggest that the synovial milieu, by providing lubrication of cartilage surfaces, impairs cartilage--cartilage integration.
Scalable Production and Isolation of Extracellular Vesicles: Available Sources and Lessons from Current Industrial Bioprocesses (2019)

Potential applications of extracellular vesicles (EVs) are attracting increasing interest in the fields of medicine, cosmetics, and nutrition. However, the manufacturing of EVs is currently characterized by low yields. This limitation severely hampers progress in research at the laboratory and clinical scales, as well as the realization of successful and cost‐effective EV‐based products. Moreover, the high level of heterogeneity of EVs further complicates reproducible manufacturing on a large scale. In this review, possible directions toward the scalable production of EVs are discussed. In particular, two strategies are considered: i) the optimization of upstream unit operations and ii) the exploitation of well‐established and mature technologies already in use in other industrial bioprocesses.
Computation of the Internet Checksum via Incremental Update (1994)

This memo describes an updated technique for incremental computation of the standard Internet checksum. It updates the method described in RFC 1141.
Effect of Fluticasone in Severe Polyposis (1998)

Fluticasone and beclomethasone aqueous nasal sprays are effective in treating the symptoms of severe nasal polyps. There was some evidence that the group treated with FPANS responded more quickly to intervention and that the magnitude of the response was greater than in the group receiving beclomethasone.
DNA Interaction of the Tyrosine Protein Kinase Inhibitor PD153035 and Its N-Methyl Analogue (2001)

The brominated anilinoquinazoline derivative PD153035 exhibits a very high affinity and selectivity for the epidermal growth factor receptor tyrosine kinase (EGF-R TK) and shows a remarkable cytotoxicity against several types of tumor cell lines. In contrast, its N-methyl derivative, designated EBE-A22, has no effect on EGF-R TK but maintains a high cytotoxic profile. The present study was performed to explore the possibility that PD153035 and its N-methyl analogue might interact with double-stranded DNA, which is a primary target for many conventional antitumor agents. We studied the strength and mode of binding to DNA of PD153035 and EBE-A22 by means of absorption, fluorescence, and circular and linear dichroism as well as by a relaxation assay using human DNA topoisomerases. The results of various optical and gel electrophoresis techniques converge to show that both drugs bind to DNA and behave as typical intercalating agents. In particular, EBE-A22 unwinds supercoiled plasmid, stabilizes duplex DNA against heat denaturation, and produces negative CD and ELD signals, as expected for an intercalating agent. Extensive DNase I footprinting experiments performed with a large range of DNA substrates show that EBE-A22, but not PD153035, interacts preferentially with GC-rich sequences and discriminates against homooligomeric runs of A and T which are often cut more readily by the enzyme in the presence of the drug compared to the control. Altogether, the results provide the first experimental evidence that DNA is a target of anilinoquinazoline derivatives and suggest that this N-methylated ring system is a valid candidate for the development of DNA-targeted cytotoxic compounds. The possible relevance of selective DNA binding to activity is considered. The unexpected GC-selective binding properties of EBE-A22 entreat further exploration into the use of N-methylanilinoquinazoline derivatives as tools for designing sequence-specific DNA binding ligands.
DETECTION, ASSAY, AND PRELIMINARY PURIFICATION OF THE PIGMENT CONTROLLING PHOTORESPONSIVE DEVELOPMENT OF PLANTS (1959)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.