gebhart/patrepeval huggingface dataset:
Ultrahigh Error Threshold for Surface Codes with Biased Noise (2018)

We show that a simple modification of the surface code can exhibit an enormous gain in the error correction threshold for a noise model in which Pauli Z errors occur more frequently than X or Y errors. Such biased noise, where dephasing dominates, is ubiquitous in many quantum architectures. In the limit of pure dephasing noise we find a threshold of 43.7(1)% using a tensor network decoder proposed by Bravyi, Suchara, and Vargo. The threshold remains surprisingly large in the regime of realistic noise bias ratios, for example 28.2(2)% at a bias of 10. The performance is, in fact, at or near the hashing bound for all values of the bias. The modified surface code still uses only weight-4 stabilizers on a square lattice, but merely requires measuring products of Y instead of Z around the faces, as this doubles the number of useful syndrome bits associated with the dominant Z errors. Our results demonstrate that large efficiency gains can be found by appropriately tailoring codes and decoders to realistic noise models, even under the locality constraints of topological codes.
Pharmacology of MK-0591 (3-[1-(4-chlorobenzyl)-3-(t-butylthio)-5-(quinolin-2-yl-methoxy)-indol-2-yl]-2,2-dimethyl propanoic acid), a potent, orally active leukotriene biosynthesis inhibitor (1992)

MK-0591 (3-[1-(4-chlorobenzyl)-3-(t-butylthio)-5-(quinolin-2-yl-methoxy)- indol-2-yl]-2,2-dimethyl propanoic acid, previously L-686,708) is a potent inhibitor of leukotriene (LT) biosynthesis in intact human and elicited rat polymorphonuclear leukocytes (PMNLs) (IC50 values 3.1 and 6.1 nM, respectively) and in human, squirrel monkey, and rat whole blood (IC50 values 510, 69, and 9 nM, respectively). MK-0591 had no effect on rat 5-lipoxygenase. MK-0591 has a high affinity for 5-lipoxygenase activating protein (FLAP) as evidenced by an IC50 value of 1.6 nM in a FLAP binding assay and inhibition of the photoaffinity labelling of FLAP by two different photoaffinity ligands. Inhibition of activation of 5-lipoxygenase was shown through inhibition of the translocation of the enzyme from the cytosol to the membrane in human PMNLs. MK-0591 was a potent inhibitor of LT biosynthesis in vivo, first, following ex vivo challenge of blood obtained from treated rats and squirrel monkeys, second, in a rat pleurisy model, and, third, as monitored by inhibition of the urinary excretion of LTE4 in antigen-challenged allergic sheep. Inhibition of antigen-induced bronchoconstriction by MK-0591 was observed in inbred rats pretreated with methysergide, Ascaris-challenged squirrel monkeys, and Ascaris-challenged sheep (early and late phase response). These results indicate that MK-0591 is a potent inhibitor of LT biosynthesis both in vitro and in vivo indicating that the compound will be suitable for assessing the role of leukotrienes in pathological situations.
A Novel Porphyromonas gingivalis FeoB Plays a Role in Manganese Accumulation (2005)

FeoB is an atypical transporter that has been shown to exclusively mediate ferrous ion transport in some bacteria. Unusually the genome of the periodontal pathogen Porphyromonas gingivalis has two genes (feoB1 and feoB2) encoding FeoB homologs, both of which are expressed in bicistronic operons. Kinetic analysis of ferrous ion transport by P. gingivalis W50 revealed the presence of a single, high affinity system with a K(t) of 0.31 microM. FeoB1 was found to be solely responsible for this transport as energized cells of the isogenic FeoB1 mutant (W50FB1) did not transport radiolabeled iron, while the isogenic FeoB2 mutant (W50FB2) transported radiolabeled iron at a rate similar to wild type. This was reflected in the iron content of W50FB1 grown in iron excess conditions which was approximately half that of the wild type and W50FB2. The W50FB1 mutant had increased sensitivity to both oxygen and hydrogen peroxide and was avirulent in an animal model of infection whereas W50FB2 exhibited the same virulence as the wild type. Analysis of manganous ion uptake using inductively coupled plasma-mass spectrometry revealed a greater than 3-fold decrease in intracellular manganese accumulation in W50FB2 which was also unable to grow in manganese-limited media. The protein co-expressed with FeoB2 appears to be a novel FeoA-MntR fusion protein that exhibits homology to a manganese-responsive, DNA-binding metalloregulatory protein. These results indicate that FeoB2 is not involved in iron transport but plays a novel role in manganese transport.
Protective effects of a leukotriene inhibitor and a leukotriene antagonist on endotoxin-induced mortality in carrageenan-pretreated mice (1992)

The leukotrienes and tumor necrosis factor (TNF) play an important role in the pathophysiology of septic shock, in which hypotension, leukopenia, thrombocytopenia, and hemoconcentration are observed. This study was performed to examine the effects of a 5-lipoxygenase inhibitor (AA-861), a selective leukotriene receptor antagonist (ONO-1078), and a cyclooxygenase inhibitor (indomethacin) on endotoxin-induced mortality and TNF production in mice. Mice were injected intraperitoneally with carrageenan (5 mg per mouse), which we previously reported as an effective priming agent for lipopolysaccharide (LPS)-induced TNF production and mortality (M. Ogata, S. Yoshida, M. Kamochi, A. Shigematsu, and Y. Mizuguchi, Infect. Immun. 59:679-683, 1991). The indicated doses of AA-861, ONO-1078, indomethacin, or controls were administrated subcutaneously 30 min before LPS (50 micrograms per mouse) provocation. The mortality of mice was significantly decreased by pretreatment with AA-861 (P less than 0.001) or ONO-1078 (P less than 0.01) but not by pretreatment with indomethacin. The 50% lethal dose of LPS in the mice treated with dimethyl sulfoxide or ethanol was 32 or 33 micrograms, respectively, and it increased to 83 micrograms with AA-861 or 59 micrograms with ONO-1078, respectively. Neither AA-861 nor ONO-1078 suppressed LPS-induced TNF production in sera. Treatment with AA-861 significantly decreased the leukopenia and thrombocytopenia, and ONO-1078 significantly decreased the hemoconcentration and thrombocytopenia. The role of endogenous TNF was also examined in the carrageenan-pretreated mice. Treatment with 2 x 10(5) U of rabbit anti TNF-alpha antibody intravenously 2 h before LPS challenge significantly suppressed the LPS-induced TNF activity and decreased the mortality. Therefore, both leukotrienes and TNF play important roles in endotoxin-induced shock and mortality.
Stress proteins are immune targets in leprosy and tuberculosis. (1988)

To understand the immune response to infection by tuberculosis and leprosy bacilli and to develop improved vaccines, the nature of antigens that are involved in humoral and cell-mediated immunity was investigated. We have determined that five immunodominant protein antigens under study are homologues of stress proteins. This finding and observations with other pathogens suggest that infectious agents may respond to the host environment by producing stress proteins and that these proteins can be important immune targets. We postulate that abundant and highly conserved stress proteins may have "immunoprophylactic" potential for a broad spectrum of human pathogens.
Use of Boar Spermatozoa for Artificial Insemination II. Fertilizing Capacity of Fresh and Frozen Spermatozoa in Gilts Inseminated Either at a Fixed Time or According to Walsmeta Readings (1982)

A fertility trial was conducted comparing two methods of defining the optimum time to inseminate frozen boar semen. One hundred sixty-four gilts were inseminated, one-half at a fixed insemination time of 32 to 34 h after calculated onset of estrus and the remainder were inseminated on the basis of changes in the vaginal mucosal electrical resistance. Inseminations were made when the instrument (an inversely scaled ohmmeter) reading fell between 54 to 64 on a scale of 1 to 100. Both fresh and frozen boar semen were used. Pregnancy rates and live embryos/gilts from inseminations made at the fixed time and inseminations made on the basis of ohmmeter readings did not differ significantly for either fresh of frozen-thawed spermatozoa. Pregnancy rates and number of live embryos/gilt were significantly higher for gilts inseminated with fresh spermatozoa than for those inseminated with frozen-thawed spermatozoa (82%, 11.6 vs 61%, 8.2, respectively). Inseminations were conducted from January to September. Pregnancy rates were significantly higher for inseminations made for the first quarter or the year (January, February and March) than for inseminations made for the third quarter (July, August and September). No benefit was derived from using an ohmmeter to time insemination with frozen-thawed boar spermatozoa.
Analysis of the physical state of different human papillomavirus DNAs in intraepithelial and invasive cervical neoplasm (1991)

The integration of human papillomavirus (HPV) DNA into the human genome has been generally accepted as a characteristic of malignant lesions. To gain a better understanding of this phenomenon, genomic DNA from 181 cervical biopsy specimens was isolated and analyzed for HPV type and physical state of the HPV genome. These specimens represented the full spectrum of cervical disease, from condyloma to invasive carcinoma. Discrimination between integrated and episomal HPV DNA was accomplished by the detection of HPV-human DNA junction fragments on Southern blots. In most cases in which ambiguous Southern blot results were obtained, the specimens were reanalyzed by two-dimensional gel electrophoresis. Of the 100 biopsy specimens of cervical intraepithelial neoplasia analyzed, only 3 showed integrated HPV DNA, in contrast to 56 (81%) of 69 cervical carcinomas (P less than 0.001) showing integrated HPV DNA. Of the 40 carcinomas containing HPV 16 DNA, 29 (72%) had integrated HPV DNA, of which 8 (20%) also had episomal HPV DNA. In 11 (27%) cancers, only episomal HPV 16 DNA was detected. All 23 HPV 18-containing carcinomas had integrated HPV DNA, and 1 also had episomal HPV 18 DNA. The difference between HPV types 16 and 18 with respect to frequency of integration was statistically significant (P less than 0.01). The results of this study indicate that detectable integration of HPV DNA, regardless of type, occurs infrequently in cervical intraepithelial neoplasia. The absence of HPV 16 DNA integration in some carcinomas implies that integration is not always required for malignant progression. In contrast, the consistent integration of HPV 18 DNA in all cervical cancers examined may be related to its greater transforming efficiency in vitro and its reported clinical association with more aggressive cervical cancers.
Inosine analogs. Their metabolism in mouse L cells and in Leishmania donovani. (1985)

The growth of Leishmania donovani promastigotes and mouse L cells is differentially inhibited by several inosine analogs with modifications in the imidazole ring. The protozoal and mammalian cells also demonstrate differential metabolism of these analogs. 7-Deazainosine, 7-thia-7,9-dideazainosine, and formycin B were converted to their respective ATP analogs by both cell types. 8-Azainosine was converted to a GTP analog by mouse L cells; L. donovani did not metabolize this nucleoside. 9-Deazainosine and allopurinol riboside were metabolized only to their respective IMP analogs by L cells. L. donovani metabolized 9-deazainosine and allopurinol riboside to their ATP analogs and also metabolized 9-deazainosine to its GTP analog. All nucleosides studied were resistant to cleavage by either organism. From metabolism studies in the presence of a specific enzyme inhibitor, it was deduced that allopurinol riboside, formycin B, and 9-deazainosine were phosphorylated by at least two different routes in the mouse L cells. The metabolism of formycin B was inhibited 65% by the adenosine kinase inhibitor, 5-iodotubercidin, whereas the metabolism of allopurinol riboside (14% inhibition) and 9-deazainosine (0% inhibition) was only slightly affected by this inhibitor. The metabolism of allopurinol riboside and 9-deazainosine by L. donovani was not affected by 5-iodotubercidin. In contrast to the results of L cells, the metabolism of formycin B by L. donovani was also not affected by 5-iodotubercidin. The abilities of mouse L cells and L. donovani to metabolize these inosine analogs to the corresponding nucleotide analogs of ATP or GTP may be considered to be an activating step and correlates well with the respective cytotoxic effects of these compounds.
Progress from clinical trials on breast cancer (1994)

The current management of carcinoma of the breast is very different than it was a relatively few years ago. The improvements in care have been introduced into practice as a result of clinical trials. From the nonrandomized but controlled clinical trial of radical mastectomy by William S. Halsted demonstrating that locoregional control could be dramatically improved, trials have become considerably more sophisticated in both design and analysis. Randomized clinical trials of breast conservation therapy were begun in Milan by Dr. Veronesi. Trials by the National Surgical Adjuvant Breast and Bowel Program headed by Dr. Bernard Fisher have, with other trials, defined the benefits and techniques of this less morbid treatment approach. Improvements in survival have also emerged from randomized clinical trials of adjuvant systemic therapy. Although these improvements are significant, they do not eliminate the risk of death from breast cancer. Much remains to be answered in the clinical management of breast cancer. Clinical trials will assess new developments and introduce improvements to clinical practice. Funding for research in breast cancer must support basic investigation into the biology of the disease process, new approaches to control disease, and clinical trials to test therapeutic principles and techniques.
Impact of Preexisting Vector Immunity on the Efficacy of Adeno-Associated Virus-Based HIV-1 Gag Vaccines (2008)

Vectors based on primate-derived adeno-associated virus (AAV) are being considered in the development of genetic vaccines against a number of diseases including infection with HIV-1. Preexisting immunity to the vaccine carrier as a result of natural infections could potentially compromise vaccine efficacy. This study evaluates the impact of neutralizing antibodies against AAV capsids on the ability of HIV-1 Gag-expressing vectors to elicit transgene-specific T and B cell responses. Mice were passively transferred with pooled human immunoglobulin at various doses to simulate human antivector humoral immunity. Vectors based on serotype 2, which were evaluated in the clinic, were compared with those created from the novel monkey isolates AAV7 and AAV8. Inhibition of AAV2-directed Gag responses occurred at doses of human immunoglobulin 10- to 20-fold less than was required to inhibit immunogenicity of AAV7 and AAV8 vectors. Cynomolgus macaques were screened for preexisting immunity to AAV7 and AAV8 and sera from individual animals were passively transferred into mice that were analyzed for AAV vaccine efficacy. There was a correlation between the level of preexisting capsid neutralizing titers and diminution of vaccine efficacy; sera from a number of animals with no detectable neutralizing antibodies showed partial vaccine inhibition, suggesting that the in vitro assay is less sensitive than the in vivo passive transfer assay for detecting neutralizing antibodies to AAV.
International remote monitoring project Argentina Nuclear Power Station Spent Fuel Transfer Remote Monitoring System (1997)

The Autoridad Regulataria Nuclear (ARN) and the United States Department of Energy (DOE) are cooperating on the development of a Remote Monitoring System for nuclear nonproliferation efforts. A Remote Monitoring System for spent fuel transfer will be installed at the Argentina Nuclear Power Station in Embalse, Argentina. The system has been designed by Sandia National Laboratories (SNL), with Los Alamos National Laboratory (LANL) and Oak Ridge National Laboratory (ORNL) providing gamma and neutron sensors. This project will test and evaluate the fundamental design and implementation of the Remote Monitoring System in its application to regional and international safeguards efficiency. This paper provides a description of the monitoring system and its functions. The Remote Monitoring System consists of gamma and neutron radiation sensors, RF systems, and video systems integrated into a coherent functioning whole. All sensor data communicate over an Echelon LonWorks Network to a single data logger. The Neumann DCM 14 video module is integrated into the Remote Monitoring System. All sensor and image data are stored on a Data Acquisition System (DAS) and archived and reviewed on a Data and Image Review Station (DIRS). Conventional phone lines are used as the telecommunications link to transmit on-site collected data and images to remote locations. The data and images are authenticated before transmission. Data review stations will be installed at ARN in Buenos Aires, Argentina, ABACC in Rio De Janeiro, IAEA Headquarters in Vienna, and Sandia National Laboratories in Albuquerque, New Mexico. 2 refs., 2 figs.
Pharmacological therapies for autism spectrum disorder: a review. (2015)

Medications are often added to behavioral therapy to help patients with autism spectrum disorder function successfully. This review discusses approved and off-label pharmacotherapeutic options for the various symptoms of the disorder.
Meta‐Analysis of Steady‐State Pharmacokinetics of Troglitazone and Its Metabolites (1997)

The object of this study is to evaluate the effects of age, gender, age-by-gender interaction, Type II diabetes, body weight, race, smoking, and formulation on steady-state pharmacokinetics of troglitazone, Metabolite 1 (sulfate conjugate), and Metabolite 3 (quinone metabolite) following multiple-dose oral administration of troglitazone. Pharmacokinetic parameter estimates [Cl/F (apparent oral clearance), AUC0-24 (area under plasma concentration-time curve), and ratio of AUC for troglitazone to Metabolite 1 and to Metabolite 3] obtained from 84 healthy volunteers and 171 patients with Type II diabetes in 8 studies were analyzed using a graphical method (for race and smoking) or a weighted ANCOVA model incorporating gender, health status (healthy vs Type II diabetes), and formulation as main effects; age, age-by-gender interaction, and body weight as continuous covariates. Ratio of AUC for troglitazone to metabolites was also examined by inspection of log-probit plots. Age, gender, age-by-gender, Type II diabetes, and formulation had negligible effects on troglitazone Cl/F, AUC0-24 (all analytes), and AUC ratio of troglitazone to metabolites. Race and smoking did not appear to influence steady-state pharmacokinetics of troglitazone and its metabolites. Although body weight was a significant covariate for AUC0-24 and Cl/F, the explanatory power of the overall model was weak (R2 < 0.2). Log-probit plots did not reveal a polymorphic distribution in AUC ratio of troglitazone to Metabolite 1 or Metabolite 3. Based on pharmacokinetics, dose adjustment for troglitazone in relation to the demographic factors examined is not required due to their poor predictive ability on steady-state pharmacokinetics of troglitazone and its metabolites.
Simulation of magnetoresistive response in a small Permalloy strip (1993)

A micromagnetic simulation program has been used to calculate the magnetoresistance of a free-standing 4 μm×1 μm×200 Å Permalloy strip for a variety of numerical hysteresis loops in which a constant bias field is applied along the easy axis and a variable field is applied along the hard, in-plane axis. The main purpose of this study is to correlate noise in the magnetoresistive response with micromagnetic behavior and to show that the noise is considerably reduced by the application of the bias field. Two different methods for evaluating the magnetoresistive response are discussed.
Binding of [acetyl-14C] Trichodermin to the Peptidyl Transferase Centre of Eukaryotic Ribosomes (1974)

The antibiotic trichodermin, an inhibitor of the peptidyl transferase centre of eukaryotic ribosomes, was synthesized radioactively labeled. [acetyl-14C]Trichodermin (15.4 mCi/mmol) was obtained. [acetyl-14C]Trichodermin binds to ribosomes from yeast with a dissociation constant of 1.8 μM and to ribosomes of human tonsils with a dissociation constant of 0.67 μM but it does not bind to ribosomes of Escherichia coli. Similarly, the antibiotic binds to 60-S subunits derived from yeast ribosomes with a dissociation constant of 1.4 μM. A single-site interaction was observed in all cases. Trichodermin and anisomycin compete for binding to the peptidyl transferase centre. Although the activity of this centre is much affected by ionic conditions, the specific site of trichodermin interaction appears to be less sensitive since changes in ionic conditions, pH and ethanol concentration hardly modify the extent of antibiotic binding. Trichodermin binding to eukaryotic ribosomes is inhibited not only by anisomycin, but also by tenuazonic acid and a number of sesquiterpene antibiotics of the trichodermin group (tricho-dermol, trichothecin, fusarenon X and verrucarin A).
Development of a highly specialized cDNA array for the study and diagnosis of epithelial ovarian cancer. (2002)

Ovarian cancer is a major cause of cancer death in women. Unfortunately, the molecular pathways underlying ovarian cancer progression are poorly understood, making the development of novel diagnostic and therapeutic strategies difficult. On the basis of our previous observations obtained from serial analysis of gene expression, we have constructed a specialized cDNA array for the study of ovarian cancer. Small, specialized arrays have several practical advantages and can reveal information that is lost in the "noise" generated by irrelevant genes present in larger arrays. The array, which we named Ovachip, contains 516 cDNAs chosen from our serial analysis of gene expression and cDNA array studies for their relevance to ovarian cancer. The gene expression patterns revealed with the Ovachip are highly reproducible and extremely consistent among the different ovarian specimens tested. This array was extremely sensitive at differentiating ovarian cancer from colon cancer based on expression profiles. The Ovachip revealed clusters of coordinately expressed genes in ovarian cancer. One such cluster, the IGF2 cluster, is particularly striking and includes the insulin-like growth factor II, the cisplatin resistance-associated protein, the checkpoint suppressor 1, the cyclin-dependent kinase 6, and a protein tyrosine phosphatase receptor. We also identified a cluster of down-regulated genes that included the cyclin-dependent kinase 7 and cyclin H. Thus, the Ovachip allowed us to identify previously unidentified clusters of differentially expressed genes that may provide new paradigms for molecular pathways important in ovarian malignancies. Because of the relevance of the arrayed genes, the Ovachip may become a powerful tool for investigators in the field of ovarian cancer and may facilitate progress in understanding the etiology of this disease and in its clinical management.