gebhart/patrepeval huggingface dataset:
An Automated Fluorescent PCR Method for Detection of Shiga Toxin-Producing Escherichia coli in Foods (1998)

An automated fluorescence-based PCR system (a model AG-9600 AmpliSensor analyzer) was investigated to determine whether it could detect Shiga toxin-producing Escherichia coli (STEC). The AmpliSensor PCR assay involves amplification-mediated disruption of a fluorogenic DNA signal duplex (AmpliSensor) that is homologous to conserved target sequences in a 323-bp amplified fragment of Shiga toxin genes stx1, stx2, and stxe. Using the Amplisensor assay, we detected 113 strains of STEC belonging to 50 different serotypes, while 18 strains of non-Shiga-toxin-producing E. coli and 68 strains of other bacteria were not detected. The detection limits of the assay were less than 1 to 5 CFU per PCR mixture when pure cultures of five reference strains were used and 3 CFU per 25 g of food when spiked ground beef samples that were preenriched overnight were used. The performance of the assay was also evaluated by using 53 naturally contaminated meat samples and 48 raw milk samples. Thirty-two STEC-positive samples that were confirmed to be positive by the culture assay were found to be positive when the AmpliSensor assay was used. Nine samples that were found to be positive when the PCR assay was used were culture negative. The system described here is an automated PCR-based system that can be used for detection of all serotypes of STEC in food or clinical samples.
Surpassing Tradeoffs by Separation: Examples in Frequency Generation Circuits (2008)

We review three examples (two PLLs [Crowley, 1979; Woo et al.] and one on-chip transmission-line resonator [Andress and Ham, 2005] ) of design tradeoffs which can in fact be circumvented; the key in each case is that the parameters that seem to trade off with each other are actually separated in time or space. This paper is an attempt to present these designs in such a way that this common approach can hopefully be applied to other circuits.
Primary structure and expression of a naturally truncated human P2X ATP receptor subunit from brain and immune system (1997)

A novel member of the ionotropic ATP receptor gene family has been identified in human brain. This 422 amino acid long P2X receptor subunit has 62% sequence identity with rat P2X5. Several characteristic motifs of ATP-gated channels are present in its primary structure, but this P2X5-related subunit displays a single transmembrane domain. Heterologous expression of chimeric subunits containing the C-terminal domain of rat P2X5 leads to the formation of desensitizing functional ATP-gated channels in Xenopus oocytes. The developmentally regulated mRNA, found in two splicing variant forms, is expressed at high levels in brain and immune system.
44. Organic phosphorus compounds. Part I. The reaction of dialkyl methylphosphonates and methylphosphonothionates with inorganic acid chlorides (1961)

The first page of this article is displayed as the abstract.
Invasive phenotype of MCF10A cells overexpressing c‐Ha‐ras and c‐erbB‐2 oncogenes (1995)

Infection with erbB-2 (E) of Ha-ras (H) oncogene-transfected cells has been previously shown to cooperatively induce anchorage-independent growth of the MCF10A human mammary epithelial cell line in vitro, but not to induce nude mouse tumorigenicity. Here we show that oncogene-transformed MCF10A are able to halt in the lungs of nude mice, a sign of organ colonization potential. We have therefore studied the transformants for in vitro migratory and invasive properties known to correlate with the metastatic potential of human mammary carcinoma cells in nude mice. MCF10A transfected with Ha-ras, infected with a recombinant retroviral vector containing the human c-erB-2 proto-oncogene (MCF10A-HE cells), show a higher invasive index than either the single transfectant (MCF10A-H) or MCF10A-erB-2(MCF10A-E) cells in the Boyden chamber chemotaxis and chemoinvasion assays. The MCF10A-HE cells also adopted an invasive stellate growth pattern when plated or embedded in Matrigel, in contrast to the spherical colonies formed by the single transformants MCF10A-H, MCF10A-E, and the parental cells. Dot-blot analysis of gelatinase A and TIMP-2 mRNA levels revealed increasing gelatinase A mRNA levels (HE > E > H > MCF10A) and reduced TIMP-2 expression in both single and double transformants. Furthermore, MCF10A-HE cells show more MMP-2 activity than parental MCF10A cells or the single transformants. CD44 analysis revealed differential isoform banding for the MCF10A-HE cells compared to parental cells, MCF10A-H and MCF10A-E, accompanied by increased binding of hyaluronan by the double transformants. Our results indicate that erB-2 and Ha-ras co-expression can induce a more aggressive phenotype in vitro, representative of the malignancy of mammary carcinomas.
Biological Effects and Metabolic Rates of Glucagonlike Peptide-1 7–36 Amide and Glucagonlike Peptide-1 7–37 in Healthy Subjects Are Indistinguishable (1993)

The biological effects and the metabolism of the intestinal hormone glucagonlike peptide-1 7-36 amide and glucagonlike peptide-1 7-37 were studied in normal healthy subjects. GLP-1 7-36 amide and GLP-1 7-37 equipotently stimulated insulin secretion (integrated hormone response 0-60 min, 631 +/- 211 vs. 483 +/- 177 pmol/h x L-1) and C-peptide secretion (integrated hormone response 9064 +/- 1804 vs. 9954 +/- 2031 pmol/h x L-1) and equipotently lowered plasma glucose (integrated decrease 48.3 +/- 5.7 vs. 46.2 +/- 8.4 mmol/h x L-1) and plasma glucagon (integrated decrease 80.4 +/- 24.3 vs. 156.0 +/- 34.6 pmol/h x L-1). Both GLP-1 7-36 amide and GLP-1 7-37 lowered the plasma concentration of free fatty acids significantly. The plasma half-lives of GLP-1 7-36 amide and GLP-1 7-37 were 5.3 +/- 0.4 vs. 6.1 +/- 0.8 min, and the metabolic clearance rates of the two peptides also were similar (14.6 +/- 2.4 vs. 12.2 +/- 1.0 pmol/kg x min). In conclusion, COOH-terminal amidation is neither important for the metabolism of GLP-1 nor for its effects on the endocrine pancreas.
History of the Cosmetic Use of Botulinum A Exotoxin (1998)

1 Division of Dermatology (AC) and Department of Ophthalmology (JC), University of British Columbia, Vancouver, British Columbia, Canada. Address correspondence and reprint requests to: Alastair Carruthers, FRCPC, Skin Care Center, 835 W 10th Ave, Vancouver, BC V5Z 4EA, Canada.
Analysis of the Interaction of Surfactants Oleic Acid and Oleylamine with Iron Oxide Nanoparticles through Molecular Mechanics Modeling (2015)

The interface interactions between surfactants oleic acid and oleylamine and magnetic nanoparticles are studied via molecular mechanics and dynamics. Mixtures of these two surfactants are widely advocated in the chemical synthesis of nanoparticles. However, the exact dynamic mechanism remains unclear. Here we report, for the first time, a comprehensive qualitative model showing the importance of acid-base complex formation between oleic acid and oleylamine as well as the presence of free protons in the engineering of nanoparticles of specific shapes and sizes. We show why critical parameters such as surfactant concentration may modify iron oxide nanoparticle shape and size and how this can be understood in the light of acid-base complex pair formation. We report on the influence these parameters have on both the in situ nanoparticle surface charge and zeta potential. Transmission electron microscopy (TEM), FTIR, and pH studies are used to confirm the validity of the calculated binding energies and number of acid-base pairs.
Development of AIDS in a chimpanzee infected with human immunodeficiency virus type 1 (1997)

The condition of a chimpanzee (C499) infected with three different isolates of human immunodeficiency virus type 1 (HIV-1) for over 10 years progressed to AIDS. Disease development in this animal was characterized by (i) a decline in CD4+ cells over the last 3 years; (ii) an increase in viral loads in plasma; (iii) the presence of a virus, termed HIV-1JC, which is cytopathic for chimpanzee peripheral blood mononuclear cells; and (iv) the presence of an opportunistic infection and blood dyscrasias. Genetic analysis of the V1-V2 region of the envelope gene of HIV-1JC showed that the virus present in C499 was significantly divergent from all inoculating viruses (> or = 16% divergent at the amino acid level) and was suggestive of a large quasispecies. Blood from C499 transfused into an uninfected chimpanzee (C455) induced a rapid and sustained CD4+-cell decline in the latter animal, concomitant with high plasma viral loads. These results show that HIV-1 can induce AIDS in chimpanzees and suggest that long-term passage of HIV-1 in chimpanzees can result in the development of a more pathogenic virus.
Effect of Dissolved Oxygen on Continuous Production of Methionine (2001)

Methionine production by a mutant strain of Corynebacterium lilium was studied at different dilution rates and different dissolved oxygen concentrations, based on a statistical central composite design. The effect of dissolved oxygen levels between 2 % and 60 % and dilution rate levels between 0.04 to 0.29 on continuous production of methionine was studied. The process is described by the Leudeking-Piret model. The experimentally obtained maxima for methionine and biomass productivities, observed at the same dilution rate of 0.17 h–1, also corresponds to the theoretical prediction based on this model. This experimental observation is further supported by the surface response prediction of a dilution rate of 0.16 h–1 for maximum methionine productivity and 0.15 h–1 for cell mass productivity. Also, beyond the critical value of 30 % dissolved oxygen, the apparent benefits of oxygen transfer become less significant.
Functional Conservation of Subfamilies of Putative UDP-N-acetylgalactosamine:Polypeptide N-Acetylgalactosaminyltransferases inDrosophila, Caenorhabditis elegans, and Mammals (2002)

The completed fruit fly genome was found to contain up to 15 putative UDP-N-acetyl-alpha-d-galactosamine:polypeptide N-acetylgalactosaminyltransferase (GalNAc-transferase) genes. Phylogenetic analysis of the putative catalytic domains of the large GalNAc-transferase enzyme families of Drosophila melanogaster (13 available), Caenorhabditis elegans (9 genes), and mammals (12 genes) indicated that distinct subfamilies of orthologous genes are conserved in each species. In support of this hypothesis, we provide evidence that distinctive functional properties of Drosophila and human GalNAc-transferase isoforms were exhibited by evolutionarily conserved members of two subfamilies (dGalNAc-T1 (l(2)35Aa) and GalNAc-T11; dGalNAc-T2 (CG6394) and GalNAc-T7). dGalNAc-T1 and novel human GalNAc-T11 were shown to encode functional GalNAc-transferases with the same polypeptide acceptor substrate specificity, and dGalNAc-T2 was shown to encode a GalNAc-transferase with similar GalNAc glycopeptide substrate specificity as GalNAc-T7. Previous data suggested that the putative GalNAc-transferase encoded by l(2)35Aa had a lethal phenotype (Flores, C., and Engels, W. (1999) Proc. Natl. Acad. Sci. U. S. A. 96, 2964-2969), and this was substantiated by sequencing of three lethal alleles l(2)35Aa(HG8), l(2)35Aa(SF12), and l(2)35Aa(SF32). The finding that subfamilies of GalNAc-transferases with distinct catalytic functions are evolutionarily conserved stresses that GalNAc-transferase isoforms may serve unique biological functions rather than providing functional redundancy, and this is further supported by the lethal phenotype of l(2)35Aa.
Antibodies in Myasthenia Gravis and Related Disorders (2004)

Myasthenia gravis (MG) is caused in the majority of cases by circulating autoantibodies to the nicotinic muscle acetylcholine receptor (AChR). Several studies have now documented a higher incidence of AChR-positive MG in both men and women over age 60 years than among younger individuals (Vincent et al. JNNP in press). Since MG can be misdiagnosed as stroke or motor neuron disease in the elderly, it is likely that there is considerable underdiagnosis of MG in this age group. Fetal AChR antibodies and arthrogryposis maternal antibodies to the fetal isoform of the AChR are found in rare cases of arthrogryposis multiplex congenital. They cross the placenta and cause paralysis in the developing fetus leading to joint contractures and other deformities. Seronegative myasthenia gravis antibodies to AChRs are present in about 85% of patients with generalized disease. Antibodies to the muscle specific receptor tyrosine kinase, MuSK, are found in 0–70% of SNMG patients; those with MuSK antibodies often present with predominant ocular and bulbar weakness, or neck extensor weakness, and may be more difficult to treat effectively with conventional immunosuppression (Vincent et al. Lancet Reviews Neurology 2002). Plasma or serum from SNMG patients may also inhibit the function of AChR expressed on TE671 cells, or on the subline that expresses adult AChRs. The effect appears to be indirect, perhaps acting on another muscle surface receptor that activates a second messenger system leading to reduced AChR function. This plasma factor is not an IgG and co-purifies with IgM (Plested et al. Neurology 2002), and its target is unknown. Voltage-gated ion channels and CNS disease antibodies to the voltage-gated calcium and potassium channels are found in Lambert Eaton myasthenic syndrome and acquired neuromyotonia, respectively. Recently, we have detected very high levels of VGKC antibodies in an increasing number of patients with „limbic“ encephalitis. Many do not have evidence of peripheral neuromuscular involvement but show high signal intensity in the temporal lobe(s), seizure activity and low plasma sodium levels. These patients, who typically do not have an associated tumor, may do well after long-term immunosuppression (Vincent et al. Brain 2004).
HIV-1 functional cure: will the dream come true? (2015)

The reservoir of human immunodeficiency virus type 1 (HIV-1), a long-lived pool of latently infected cells harboring replication-competent viruses, is the major obstacle to curing acquired immune deficiency syndrome (AIDS). Although the combination antiretroviral therapy (cART) can successfully suppress HIV-1 viremia and significantly delay the progression of the disease, it cannot eliminate the viral reservoir and the patient must continue to take anti-viral medicines for life. Currently, the appearance of the 'Berlin patient', the 'Boston patients', and the 'Mississippi baby' have inspired many therapeutic strategies for HIV-1 aimed at curing efforts. However, the specific eradication of viral latency and the recovery and optimization of the HIV-1-specific immune surveillance are major challenges to achieving such a cure. Here, we summarize recent studies addressing the mechanisms underlying the viral latency and define two categories of viral reservoir: 'shallow' and 'deep'. We also present the current strategies and recent advances in the development of a functional cure for HIV-1, focusing on full/partial replacement of the immune system, 'shock and kill', and 'permanent silencing' approaches.
Human immunodeficiency virus type 1 Pr55gag and Pr160gag-pol expressed from a simian virus 40 late replacement vector are efficiently processed and assembled into viruslike particles (1990)

Human immunodeficiency virus type 1 (HIV-1) gag and pol genes were expressed by using fragments of the BH10 clone of HIV inserted into a simian virus 40 late replacement vector. An initial construct containing the entire coding regions of gag, pol, and vif produced only minute amounts of the gag precursor, Pr55gag. However, high-level expression was obtained when an additional sequence from the env gene (the rev-responsive element) was inserted 3' of vif in the correct orientation, and rev was provided in trans from a second vector. Western immunoblot analysis of transfected cells showed the presence of large amounts of both Pr55gag and Pr160gag-pol as well as all of the expected cleavage products. Electron microscopy of thin sections of transfected cells showed a multitude of viruslike particles. Both immature particles in the process of budding and particles containing the condensed core characteristic of HIV were observed. Analysis of the released viruslike particles showed the presence of active reverse transcriptase. Sucrose gradient analysis of particles produced from [3H]uridine-labeled cells indicated a peak of radioactivity which cosedimented with a peak of p24, suggesting that the particles contained RNA.
Controllable Self-Induced Passivation of Hybrid Lead Iodide Perovskites toward High Performance Solar Cells (2014)

To improve the performance of the polycrystalline thin film devices, it requires a delicate control of its grain structures. As one of the most promising candidates among current thin film photovoltaic techniques, the organic/inorganic hybrid perovskites generally inherit polycrystalline nature and exhibit compositional/structural dependence in regard to their optoelectronic properties. Here, we demonstrate a controllable passivation technique for perovskite films, which enables their compositional change, and allows substantial enhancement in corresponding device performance. By releasing the organic species during annealing, PbI2 phase is presented in perovskite grain boundaries and at the relevant interfaces. The consequent passivation effects and underlying mechanisms are investigated with complementary characterizations, including scanning electron microscopy (SEM), X-ray diffraction (XRD), time-resolved photoluminescence decay (TRPL), scanning Kelvin probe microscopy (SKPM), and ultraviolet photoemission spectroscopy (UPS). This controllable self-induced passivation technique represents an important step to understand the polycrystalline nature of hybrid perovskite thin films and contributes to the development of perovskite solar cells judiciously.
Lactic acid bacteria as probiotics. (2006)

A number of Lactobacillus species, Bifidobacterium sp, Saccharomyces boulardii, and some other microbes have been proposed as and are used as probiotic strains, i.e. live microorganisms as food supplement in order to benefit health. The health claims range from rather vague as regulation of bowel activity and increasing of well-being to more specific, such as exerting antagonistic effect on the gastroenteric pathogens Clostridium difficile, Campylobacter jejuni, Helicobacter pylori and rotavirus, neutralising food mutagens produced in colon, shifting the immune response towards a Th2 response, and thereby alleviating allergic reactions, and lowering serum cholesterol (Tannock, 2002). Unfortunately, most publications are case reports, uncontrolled studies in humans, or reports of animal or in vitro studies. Whether or not the probiotic strains employed shall be of human origin is a matter of debate but this is not a matter of concern, as long as the strains can be shown to survive the transport in the human gastrointestinal (GI) tract and to colonise the human large intestine. This includes survival in the stressful environment of the stomach - acidic pH and bile - with induction of new genes encoding a number of stress proteins. Since the availability of antioxidants decreases rostrally in the GI tract production of antioxidants by colonic bacteria provides a beneficial effect in scavenging free radicals. LAB strains commonly produce antimicrobial substance(s) with activity against the homologous strain, but LAB strains also often produce microbicidal substances with effect against gastric and intestinal pathogens and other microbes, or compete for cell surface and mucin binding sites. This could be the mechanism behind reports that some probiotic strains inhibit or decrease translocation of bacteria from the gut to the liver. A protective effect against cancer development can be ascribed to binding of mutagens by intestinal bacteria, reduction of the enzymes beta-glucuronidase and beta-glucosidase, and deconjugation of bile acids, or merely by enhancing the immune system of the host. The latter has attracted considerable interest, and LAB have been tested in several clinical trials in allergic diseases. Characteristics ascribed to a probiotic strain are in general strain specific, and individual strains have to be tested for each property. Survival of strains during production, packing and storage of a viable cell mass has to be tested and declared.
The Optimal Reward Baseline for Gradient-Based Reinforcement Learning (2013)

There exist a number of reinforcement learning algorithms which learnby climbing the gradient of expected reward. Their long-runconvergence has been proved, even in partially observableenvironments with non-deterministic actions, and without the need fora system model. However, the variance of the gradient estimator hasbeen found to be a significant practical problem. Recent approacheshave discounted future rewards, introducing a bias-variance trade-offinto the gradient estimate. We incorporate a reward baseline into thelearning system, and show that it affects variance without introducingfurther bias. In particular, as we approach the zero-bias,high-variance parameterization, the optimal (or variance minimizing)constant reward baseline is equal to the long-term average expectedreward. Modified policy-gradient algorithms are presented, and anumber of experiments demonstrate their improvement over previous work.
Mobilization of hematopoietic stem cells with the novel CXCR4 antagonist POL6326 (balixafortide) in healthy volunteers—results of a dose escalation trial (2017)

Balixafortide is safe, well tolerated, and induces efficient mobilization of HSPCs in healthy male volunteers. Based on experience with current apheresis technology, the observed mobilization at doses ≥1500 µg/kg of balixafortide is predicted to yield in a single apheresis a standard dose of 4× 10E6 CD34+ cells/kg from most individuals donating for an approximately weight-matched recipient. Exploration of alternative dosing regimens may provide even higher mobilization responses. Trial Registration European Medicines Agency (EudraCT-Nr. 2011-003316-23) and clinicaltrials.gov (NCT01841476).
Treatment of tardive dyskinesia with levetiracetam in a transplant patient (2007)

Tardive dyskinesia may be quite disabling and options include withdrawal of offending medication, or use of tetrabenazine or reserpine. Several reports also suggested improvement of tardive movement disorders with levetiracetam. In our patient, levetiracetam relieved symptoms of tardive dyskinesia and allowed continuous use of metoclopramide. Larger studies are needed to confirm its efficacy.
The precedence effect (1999)

In a reverberant environment, sounds reach the ears through several paths. Although the direct sound is followed by multiple reflections, which would be audible in isolation, the first-arriving wavefront dominates many aspects of perception. The "precedence effect" refers to a group of phenomena that are thought to be involved in resolving competition for perception and localization between a direct sound and a reflection. This article is divided into five major sections. First, it begins with a review of recent work on psychoacoustics, which divides the phenomena into measurements of fusion, localization dominance, and discrimination suppression. Second, buildup of precedence and breakdown of precedence are discussed. Third measurements in several animal species, developmental changes in humans, and animal studies are described. Fourth, recent physiological measurements that might be helpful in providing a fuller understanding of precedence effects are reviewed. Fifth, a number of psychophysical models are described which illustrate fundamentally different approaches and have distinct advantages and disadvantages. The purpose of this review is to provide a framework within which to describe the effects of precedence and to help in the integration of data from both psychophysical and physiological experiments. It is probably only through the combined efforts of these fields that a full theory of precedence will evolve and useful models will be developed.