gebhart/patrepeval huggingface dataset:
PHASE I TRIAL OF 16 FORMULATIONS OF A TETRAVALENT LIVE-ATTENUATED DENGUE VACCINE (2003)

Laboratory-attenuated strains of each of the four dengue serotypes previously tested as monovalent vaccines in volunteers were combined and tested for immunogenicity, safety, and reactogenicity in 16 dosage combinations. Tetravalent vaccines made using combinations of high (10(5-6) plaque-forming units [PFU]/dose) or low (10(3.5-4.5) PFU/dose) dosage formulations of each of the four viruses were inoculated in 64 flavivirus non-immune adult volunteers to determine which, if any, formulation raised neutralizing antibodies in at least 75% of volunteers to at least three of four dengue serotypes following one or two inoculations. Such formulations, if safe and sufficiently non-reactogenic, would be considered for an expanded Phase II trial in the future. Formulations 1-15 were each inoculated into three or four volunteers (total = 54) on days 0 and 28. Formulation 16 was tested in 10 volunteers, five volunteers inoculated on days 0 and 30, one volunteer on days 0 and 120, and four volunteers on days 0, 30, and 120. Blood was drawn for serologic assays immediately before and one month after each vaccination, and for viremia assay on day 10 after each vaccination. The 16 formulations were safe, but variably reactogenic after the first vaccination, and nearly non-reactogenic after the second and third vaccinations. Reactogenicity was positively correlated with immunogenicity. Similar proportions of volunteers seroconverted to dengue-1 (69%), dengue-2 (78%), and dengue-3 (69%), but significantly fewer volunteers seroconverted to dengue-4 (38%). The geometric mean 50% plaque reduction neutralization test titers in persons who seroconverted were significantly higher to dengue-1 (1:94) than to dengue-2 (1:15), dengue-3 (1:10), and dengue-4 (1:2). Seven formulations met the serologic criteria required for an expanded trial, and three of these were sufficiently attenuated clinically to justify further testing.
A general characterization and simulation method for deposition and etching technology (1992)

A topography simulation system and a six-parameter unified process model are proposed for general characterization of deposition and etching technology. This system is fit to use experimentally. This model precisely expresses the process characteristics of deposition and etching equipment. A surface movement vector calculation method suitable for the unified process model is also given. This method is used for calculating cross-sectional profiles including convex and concave corners, and for general LSI processes where deposition and etching reactions occur simultaneously. The parameters can be extracted from experimental results. The extraction method is also introduced. The simulated results agree well with the experimental ones of sputter deposition and bias-ECR (electron cyclotron resonance) deposition.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
T90/44 (9.3 antigen). A cell surface molecule with a function in human T cell activation (1986)

T90/44 is a cell surface antigen which is present on human T cells of the helper and cytotoxic subsets and which binds the 9.3 monoclonal antibody (9.3 mAb). It is expressed in the form of 90-kDa disulfide-bonded dimers of a 44-kDa polypeptide and of free 44-kDa subunits. The function of T90/44 was investigated in a series of T cell function assays. 9.3 mAb was found to inhibit the activation of class II-restricted cloned T helper cells derived from leprosy patients and reactive with M. leprae antigens. The inhibition was first found at 1-10 ng/ml 9.3 mAb and regularly increased with the antibody concentration. The extent of the inhibition varied among different T cell clones in proportion to the respective different levels of T90/44 expression at their cell surface. The proliferative responses of peripheral blood lymphocytes (PBL) to purified protein derivative of M. tuberculosis (PPD) and tetanus toxoid were enhanced by the 9.3 mAb resulting in up to 20-30-fold increase of [3H]-thymidine incorporation. After phytohemagglutinin-induced activation of PBL, the number of T90/44 molecules per cell expressed at the cell surface rose from day 0 to day 7 by a factor of about 10. High concentrations of 9.3 mAb (5-10 micrograms/ml) at low cell densities and in the presence of monocytes in culture media supplemented by fetal calf serum were directly mitogenic for resting lymphocytes. The cytolytic effector functions of class I-restricted cytotoxic T lymphocytes (CTL) were not modulated by 9.3 mAb. The mixed lymphocyte reactions of three class I-restricted CTL to their specific target cells were found not to be significantly influenced by 9.3 mAb. In conclusion it is proposed that an antigen-independent T cell activation pathway can be entered at T90/44.
Isolation and characterization of functional mammary gland stem cells (2003)

Significant advances in the stem-cell biology of several tissues, including the mammary gland, have occurred over the past several years. Recent progress on stem-cell fate determination, molecular markers, signalling pathways and niche interactions in haematopoietic, neuronal and muscle tissue may provide parallel insight into the biology of mammary epithelial stem cells. Taking advantage of approaches similar to those employed to isolate and characterize haematopoietic and epidermal stem cells, we have identified a mammary epithelial cell population with several stem/progenitor cell qualities. In this article, we review some recent data on mammary epithelial stem/progenitor cells in genetically engineered mouse models. We also discuss several potential molecular markers, including stem-cell antigen-1 (Sca-1), which may be useful for both the isolation of functional mammary epithelial stem/progenitor cells and the analysis of tumour aetiology and phenotype in genetically engineered mouse models. In different transgenic mammary tumour models, Sca-1 expression levels, as well as several other putative markers of progenitors including keratin-6, possess dramatically altered expression profiles. These data suggest that the heterogeneity of mouse models of breast cancer may partially reflect the selection or expansion of different progenitors.
Rapid monocyte kinetics in acute myocardial infarction are sustained by extramedullary monocytopoiesis (2012)

Monocytes (Mo) and macrophages (MΦ) are emerging therapeutic targets in malignant, cardiovascular, and autoimmune disorders. Targeting of Mo/MΦ and their effector functions without compromising innate immunity’s critical defense mechanisms first requires addressing gaps in knowledge about the life cycle of these cells. Here we studied the source, tissue kinetics, and clearance of Mo/MΦ in murine myocardial infarction, a model of acute inflammation after ischemic injury. We found that a) Mo tissue residence time was surprisingly short (20 h); b) Mo recruitment rates were consistently high even days after initiation of inflammation; c) the sustained need of newly made Mo was fostered by extramedullary monocytopoiesis in the spleen; d) splenic monocytopoiesis was regulated by IL-1β; and e) the balance of cell recruitment and local death shifted during resolution of inflammation. Depending on the experimental approach, we measured a 24 h Mo/MΦ exit rate from infarct tissue between 5 and 13% of the tissue cell population. Exited cells were most numerous in the blood, liver, and spleen. Abrogation of extramedullary monocytopoiesis proved deleterious for infarct healing and accelerated the evolution of heart failure. We also detected rapid Mo kinetics in mice with stroke. These findings expand our knowledge of Mo/MΦ flux in acute inflammation and provide the groundwork for novel anti-inflammatory strategies for treating heart failure.
Staining of cell surface human CD4 with 2'-F-pyrimidine-containing RNA aptamers for flow cytometry (1998)

We have used recombinant human CD4 presented on beads as an affinity matrix to screen a 2'-F-pyrimidine-containing RNA library with a complexity of approximately 10(14) molecules. Affinity-selected aptamers bind recombinant CD4 with low nanomolar equilibrium dissociation constants. These high-affinity aptamers conjugated to different fluorophores such as fluorescein and phycoerythrin were used to stain cells, expressing human CD4 on cell surface, for analysis by flow cytometry. Aptamers, conjugated to fluorophores, stained mouse T cells that express human CD4 on the surface, but not the control mouse T cells lacking human CD4. The control cells, however, do express mouse CD4 whose extracellular domain has 55% sequence identity to the human form. These human CD4-specific aptamers selectively stained CD4(+) T cells in a preparation of human peripheral blood mononuclear cells. These results and others suggest that aptamers are emerging as a versatile class of molecules that can be used for various diagnostic applications performed under different formats or platforms.
Posttranslational regulation of BCL2 levels in cerebellar granule cells: A mechanism of neuronal survival (2009)

Apoptosis can be modulated by K(+) and Ca(2+) inside the cell and/or in the extracellular milieu. In murine organotypic cultures, membrane potential-regulated Ca(2+) signaling through calcineurin phosphatase has a pivotal role in development and maturation of cerebellar granule cells (CGCs). P8 cultures were used to analyze the levels of expression of B cell lymphoma 2 (BCL2) protein, and, after particle-mediated gene transfer in CGCs, to study the posttranslational modifications of BCL2 fused to a fluorescent tag in response to a perturbation of K(+)/Ca(2+) homeostasis. There are no changes in Bcl2 mRNA after real time PCR, whereas the levels of the fusion protein (monitored by calculating the density of transfected CGCs under the fluorescence microscope) and of BCL2 (inWestern blotting) are increased. After using a series of agonists/antagonists for ion channels at the cell membrane or the endoplasmic reticulum (ER), and drugs affecting protein synthesis/degradation, accumulation of BCL2 was related to a reduction in posttranslational cleavage by macroautophagy. The ER functionally links the [K(+)](e) and [Ca(2+)](i) to the BCL2 content in CGCs along two different pathways. The first, triggered by elevated [K(+)](e) under conditions of immaturity, is independent of extracellular Ca(2+) and operates via IP3 channels. The second leads to influx of extracellular Ca(2+) following activation of ryanodine channels in the presence of physiological [K(+)](e), when CGCs are maintained in mature status. This study identifies novel mechanisms of neuroprotection in immature and mature CGCs involving the posttranslational regulation of BCL2.
Distinct protein degradation mechanisms mediated by Cul1 and Cul3 controlling Ci stability in Drosophila eye development (2002)

The ubiquitin-like protein, Nedd8, covalently modifies members of the Cullin family. Cullins are the major components of a series of ubiquitin ligases that control the degradation of a broad range of proteins. We found that Nedd8 modifies Cul1 in Drosophila. In Drosophila Nedd8 and Cul1 mutants, protein levels of the signal transduction effectors, Cubitus interruptus (Ci) and Armadillo (Arm), and the cell cycle regulator, Cyclin E (CycE), are highly accumulated, suggesting that the Cul1-based SCF complex requires Nedd8 modification for the degradation processes of Ci, Arm, and CycE in vivo. We further show that two distinct degradation mechanisms modulating Ci stability in the developing eye disc are separated by the morphogenetic furrow (MF) in which retinal differentiation is initiated. In cells anterior to the MF, Ci proteolytic processing promoted by PKA requires the activity of the Nedd8-modified Cul1-based SCF(Slimb) complex. In posterior cells, Ci degradation is controlled by a mechanism that requires the activity of Cul3, another member of the Cullin family. This posterior Ci degradation mechanism, which partially requires Nedd8 modification, is activated by Hedgehog (Hh) signaling and is PKA-independent.
Coinduction of c-jun gene expression and internucleosomal DNA fragmentation by ionizing radiation (1993)

Previous work has demonstrated that the cellular response to ionizing radiation includes transcriptional activation of the c-jun early response gene. The present studies demonstrate that this induction of c-jun expression is temporally related to the appearance of internucleosomal DNA fragmentation. These events were maximal at 6 h and transient after exposure to lethal doses (20 Gy) of ionizing radiation. We also demonstrate that N-acetyl-L-cysteine (NAC), an antioxidant, inhibits X-ray-induced c-jun expression and endonucleolytic DNA cleavage. These findings suggested that both events are mediated at least in part through the formation of reactive oxygen intermediates (ROIs). Since ROIs damage DNA and X-ray-induced DNA damage is associated with activation of poly(ADP-ribose) polymerase (ADPRP), we studied the effects of the ADPRP inhibitors 3-aminobenzamide (3-AB), nicotinamide, and theophylline. 3-AB blocked both X-ray-induced c-jun expression and internucleosomal DNA fragmentation. Similar findings were obtained with nicotinamide and theophylline. In contrast, 3-AB had little if any effect on induction of c-jun transcripts or DNA fragmentation induced by the alkylating agent mitomycin C. While c-jun expression is restricted to cells in G1 and G1/S phases, we have found that X-ray-induced c-jun transcripts are detectable throughout all phases of the cell cycle. The induction of internucleosomal DNA fragmentation by X-rays was also detectable throughout the cell cycle. Taken together, these results support the coinduction of c-jun transcription and internucleosomal DNA fragmentation by ionizing radiation. Similar studies were performed with H2O2 since this agent also results in the production of ROIs.(ABSTRACT TRUNCATED AT 250 WORDS)
Packet filtering in high speed networks (1999)

Introduction The commercial viability of the future Internet depends on its ability to provide differentiated service to paying customers. The existing Internet delivers only the so-called best effort (undifferentiated) service. Examples of differentiated service include firewalls for enterprise networks, bandwidth guarantees to applications, and traffic sensitive routing. These services require Internet routers to move from simple destination-based packet forwarding to a more complex form of forwarding called layer 4 switching . In layer 4 switching, each router maintains a database of packet filters, each specifying values for some key header fields. The most common fields are the IP destination address (32 bits), IP source address (32 bits), protocol type (8 bits), and port numbers (16 bits) of destination and source applications. Each field is specified as a variable length prefix. For instance, the filter&amp;lt;F25
Breathing Detection: Towards a Miniaturized, Wearable, Battery-Operated Monitoring System (2007)

This paper analyzes the main challenges associated with noninvasive, continuous, wearable, and long-term breathing monitoring. The characteristics of an acoustic breathing signal from a miniature sensor are studied in the presence of sources of noise and interference artifacts that affect the signal. Based on these results, an algorithm has been devised to detect breathing. It is possible to implement the algorithm on a single integrated circuit, making it suitable for a miniature sensor device. The algorithm is tested in the presence of noise sources on five subjects and shows an average success rate of 91.3% (combined true positives and true negatives).
Iron uptake and increased intracellular enzyme activity follow host lactoferrin binding by Trichomonas vaginalis receptors. (1984)

Lactoferrin acquisition and iron uptake by pathogenic Trichomonas vaginalis was examined. Saturation binding kinetics were obtained for trichomonads using increasing amounts of radioiodinated lactoferrin, while no significant binding by transferrin under similar conditions was achieved. Only unlabeled lactoferrin successfully and stoichiometrically competed with 125I-labeled lactoferrin binding. Time course studies showed maximal lactoferrin binding by 30 min at 37 degrees C. Data suggest no internalization of bound lactoferrin. The accumulation of radioactivity in supernatants after incubation of T. vaginalis with 125I-labeled lactoferrin and washing in PBS suggested the presence of low affinity sites for this host macromolecule. Scatchard analysis indicated the presence of 90,000 receptors per trichomonad with an apparent Kd of 1.0 microM. Two trichomonad lactoferrin binding proteins were identified by affinity chromatography and immunoprecipitation of receptor-ligand complexes. A 30-fold accumulation of iron was achieved using 59Fe-lactoferrin when compared to the steady state concentration of bound lactoferrin. The activity of pyruvate/ferrodoxin oxidoreductase, an enzyme involved in trichomonal energy metabolism, increased more than sixfold following exposure of the parasites to lactoferrin, demonstrating a biologic response to the receptor-mediated binding of lactoferrin. These data suggest that T. vaginalis possesses specific receptors for biologically relevant host proteins and that these receptors contribute to the metabolic processes of the parasites.
The CCR4 protein from Saccharomyces cerevisiae contains a leucine-rich repeat region which is required for its control of ADH2 gene expression. (1992)

The CCR4 gene from Saccharomyces cerevisiae is required for the transcription of the glucose-repressible alcohol dehydrogenase (ADH2). Mutations in CCR4 also suppress the transcription at the ADH2 and his4-912delta loci caused by defects in the SPT10 (CRE1) and SPT6 (CRE2) genes. The CCR4 gene was mapped to the left arm of chromosome I and cloned by complementation of function using previously isolated segments of chromosome I. DNA sequence analysis of the cloned gene defined CCR4 as a 2511 bp open reading frame that would encode a polypeptide of 837 amino acids. The CCR4 mRNA was found to be 2.8 kb in size and Western analysis identified CCR4 as a 95,000 D protein. Disruption of the CCR4 gene resulted in reduced levels of ADH2 expression under both glucose and ethanol growth conditions and in temperature sensitive growth on nonfermentative medium, phenotypes essentially indistinguishable from previously identified mutations in CCR4. The amino terminus of the CCR4 protein was found to be rich in glutamine residues similar to a number of genes which are required for transcription. More importantly, CCR4 showed similarity to a diverse set of proteins sharing a leucine-rich tandem repeat motif, the presence of which has been implicated in mediating protein-protein interactions. Deletions of several of the five leucine-rich repeats in CCR4 were shown to produce nonfunctional proteins indicating the importance of the repeats to CCR4 activity. This leucine-rich repeat region may mediate the contact CCR4 makes with another factor.
Promoter hypermethylation of tumor suppressor genes in urine from kidney cancer patients. (2003)

Kidney cancer confined by the renal capsule can be surgically cured in the majority of cases, whereas the prognosis for patients with advanced disease at presentation remains poor. Novel strategies for early detection are therefore needed. Molecular DNA-based tests have successfully used the genetic alterations that initiate and drive tumorigenesis as targets for the early detection of several types of cancer in bodily fluids, including urine. Using sensitive methylation-specific PCR, we screened matched tumor DNA and sediment DNA from preoperative urine specimens obtained in 50 patients with kidney tumors, representing all major histological types, for hypermethylation status of a panel of six normally unmethylated tumor suppressor genes VHL, p16/CDKN2a, p14ARF, APC, RASSF1A, and Timp-3. Hypermethylation of at least one gene was found in all 50 tumor DNAs (100% diagnostic coverage) and an identical pattern of gene hypermethylation found in the matched urine DNA from 44 of 50 patients (88% sensitivity), including 27/30 cases of stage I disease. In contrast, hypermethylation of the genes in the panel was not observed in normal kidney tissue or in urine from normal healthy individuals and patients with benign kidney disease (100% specificity). Hypermethylation of VHL was found only in clear cell, whereas hypermethylation of p14ARF, APC, or RASSF1A was more frequent in nonclear cell tumors, which suggested that the panel might facilitate differential diagnosis. We conclude that promoter hypermethylation is a common and early event in kidney tumorigenesis and can be detected in the urine DNA from patients with organ-confined renal cancers of all histological types. Methylation-specific PCR may enhance early detection of renal cancer using a noninvasive urine test.
Analyse de stratégies bayésiennes et fréquentistes pour l'allocation séquentielle de ressources (2014)

In this thesis, we study strategies for sequential resource allocation, under the so-called stochastic multi-armed bandit model. In this model, when an agent draws an arm, he receives as a reward a realization from a probability distribution associated to the arm. In this document, we consider two different bandit problems. In the reward maximization objective, the agent aims at maximizing the sum of rewards obtained during his interaction with the bandit, whereas in the best arm identification objective, his goal is to find the set of m best arms (i.e. arms with highest mean reward), without suffering a loss when drawing ‘bad’ arms. For these two objectives, we propose strategies, also called bandit algorithms, that are optimal (or close to optimal), in a sense precised below. Maximizing the sum of rewards is equivalent to minimizing a quantity called regret. Thanks to an asymptotic lower bound on the regret of any uniformly efficient algorithm given by Lai and Robbins, one can define asymptotically optimal algorithms as algorithms whose regret reaches this lower bound. In this thesis, we propose, for two Bayesian algorithms, Bayes-UCB and Thompson Sampling, a finite-time analysis, that is a non-asymptotic upper bound on their regret, in the particular case of bandits with binary rewards. This upper bound allows to establish the asymptotic optimality of both algorithms. In the best arm identification framework, a possible goal is to determine the number of samples of the armsneeded to identify, with high probability, the set of m best arms. We define a notion of complexity for best arm identification in two different settings considered in the literature: the fixed-budget and fixed-confidence settings. We provide new lower bounds on these complexity terms and we analyse new algorithms, some of which reach the lower bound in particular cases of two-armed bandit models and are therefore optimal
Mifepristone: an overview for Australian practice (2009)

ra l i a n p re s c riber.com Summary Mifepristone was the first antiprogestogen to be developed for clinical use. it is not only a progesterone receptor antagonist, but also acts as a glucocorticoid receptor antagonist. The fundamental importance of progesterone for human conception and throughout pregnancy has meant that mifepristone has been used in other countries for emergency contraception and medical abortion in the first and second trimester of pregnancy. it has also been used to manage fetal death in utero in the third trimester of pregnancy. There are other potential uses based on its mechanism of action, such as reducing the bleeding associated with uterine fibroids.