gebhart/patrepeval huggingface dataset:
Malaria vaccine development: a multi-immune response approach (1996)

Introduction Preventing sporozoite invasion of hepatocytes Attacking the infected hepatocyte Preventing effective merozoite invasion of erythrocytes Malaria Vaccines: Attacking infected erythrocytes Preventing cytoadherence of infected erythrocytes to endothelial cells and non-infected erythrocytes An anti-toxic vaccine for malaria Transmission-blocking vaccines Development and field-testing of the synthetic Spf66 malaria vaccine What can be expected from malaria vaccines Predicting the effects of vaccination on the population dynamics of malaria.
Overview of evolving strategies incorporating prostate-specific membrane antigen as target for therapy. (2000)

Prostate-specific membrane antigen (PSMA) is a potential target in prostate cancer patients because it is very highly expressed and because it has been reported to be upregulated by androgen deprivation. This overview addresses the expression of the PSMA gene in terms of the promoter and enhancer and how that may play a role in gene therapy. We also review PSMA as a target for antibodies for imaging and treatment and the development of a novel hybrid T-cell receptor that combines the specificity of anti-PSMA antibodies with that of T-cell receptor activation when introduced into primary lymphocytes by retroviral-mediated gene transfer. We also discuss our recent findings on the expression of a PSMA-like gene and how that understanding allows specific targeting of PSMA.
Allelic Association of Gene Markers on Chromosomes 5q and 11q With Atopy and Bronchial Hyperresponsiveness (1996)

To investigate genetic factors in asthma and atopy, we sought allelic associations for 12 markers near candidate loci for serum total, immunoglobulin E (IgE), and bronchial hyperresponsiveness (BHR) to inhaled histamine in 131 families comprising 685 individuals, selected randomly without regard to atopy or asthma. Nonparametric linkage and association analyses were performed with the Nonparametric Analysis of Lineage and Association (NOPAR) program, and parametric analyses were performed with the Complex Inheritance with Diathesis and Severity (COMDS) program on an ordered polychotomy of ranked scores. On chromosome 11q, allele 168 at the D11S527 locus was significantly associated with BHR (p<0.0003) but not with log IgE. At the D11S534 locus, allele 235 was significantly associated with log IgE (p = 0.007) but not with BHR. Both D11S527 and D11S534 were too distant from the gene encoding the high-affinity IgE receptor FcepsilonRIbeta to account for the association. At the interleukin-9 (IL-9) locus, the 118 allele showed significant association with serum total IgE (p<0.003) but not with histamine BHR. Parametric tests are more conservative, perhaps because they demand consistency with mendelian inheritance and tight linkage. These findings provide support for the view that both chromosomes 5 and 11 may contain genes relevant to asthma and atopy, a possible candidate being the interleukin-4 (IL-4) gene cluster. Because these associations are extremes in a large number of tests, they require confirmation in other samples.
Password practices on leading websites – revisited (2014)

Passwords are perhaps the most maligned example of security technology. People very readily dismiss them, and there is a good degree of evidence to support their reasons for doing so.1 However, while fully acknowledging that they have inherent limitations, the extent of the problem is arguably worse than it needs to be.
Alkaline phosphatase reduces hepatic and pulmonary injury in liver ischaemia–reperfusion combined with partial resection (2006)

BIAP attenuates hepatic and pulmonary injury after partial liver I/R and PHX.
Admittance Spectroscopy of ZnO Crystals Containing Ag (1991)

An experiment on admittance spectroscopy was performed on the ZnO-Ag alloy diodes, in which Ag was thought to diffuse into the ZnO crystal. It was found that Ag behaved as an acceptor in ZnO. Its energy level was 0.23 eV below the conduction band, and the electron capture cross section was about 6×10 -16 cm 2 .
Genes Involved in Long-Chain Alkene Biosynthesis in Micrococcus luteus (2009)

ABSTRACT Aliphatic hydrocarbons are highly appealing targets for advanced cellulosic biofuels, as they are already predominant components of petroleum-based gasoline and diesel fuels. We have studied alkene biosynthesis in Micrococcus luteus ATCC 4698, a close relative of Sarcina lutea (now Kocuria rhizophila ), which 4 decades ago was reported to biosynthesize iso - and anteiso -branched, long-chain alkenes. The underlying biochemistry and genetics of alkene biosynthesis were not elucidated in those studies. We show here that heterologous expression of a three-gene cluster from M . luteus (Mlut_13230-13250) in a fatty acid-overproducing Escherichia coli strain resulted in production of long-chain alkenes, predominantly 27:3 and 29:3 (no. carbon atoms: no. C＝C bonds). Heterologous expression of Mlut_13230 ( oleA ) alone produced no long-chain alkenes but unsaturated aliphatic monoketones, predominantly 27:2, and in vitro studies with the purified Mlut_13230 protein and tetradecanoyl-coenzyme A (CoA) produced the same C 27 monoketone. Gas chromatography-time of flight mass spectrometry confirmed the elemental composition of all detected long-chain alkenes and monoketones (putative intermediates of alkene biosynthesis). Negative controls demonstrated that the M . luteus genes were responsible for production of these metabolites. Studies with wild-type M . luteus showed that the transcript copy number of Mlut_13230-13250 and the concentrations of 29:1 alkene isomers (the dominant alkenes produced by this strain) generally corresponded with bacterial population over time. We propose a metabolic pathway for alkene biosynthesis starting with acyl-CoA (or-ACP [acyl carrier protein]) thioesters and involving decarboxylative Claisen condensation as a key step, which we believe is catalyzed by OleA. Such activity is consistent with our data and with the homology (including the conserved Cys-His-Asn catalytic triad) of Mlut_13230 (OleA) to FabH (β-ketoacyl-ACP synthase III), which catalyzes decarboxylative Claisen condensation during fatty acid biosynthesis.
Biodistribution and Gene Expression of Lipid/Plasmid Complexes after Systemic Administration (1998)

The objectives of this study were to investigate the influence of physicochemical properties of lipid/plasmid complexes on in vivo gene transfer and biodistribution characteristics. Formulations based on 1,2-di-O-octadecenyl-3-trimethylammonium propane (DOTMA) and novel biodegradable cationic lipids, such as ethyl dioleoyl phosphatidylcholine (EDOPC), ethyl palmitoyl myristyl phosphatidylcholine (EPMPC), myristyl myristoyl carnitine ester (MMCE), and oleyl oleoyl L-carnitine ester (DOLCE), were assessed for gene expression after tail vein injection of lipid/plasmid complexes in mice. Gene expression was influenced by cationic lipid structure, cationic lipid-to-colipid molar ratios, plasmid-to-lipid charge ratios, and precondensation liposome size. Detectable levels of human growth hormone (hGH) in serum, human factor IX (hFIX) in plasma, and chloramphenicol acetyltransferase (CAT) in the lung and liver were observed with positively charged lipid/plasmid complexes prepared from 400-nm extruded liposomes with a cationic lipid-to-colipid ratio of 4:1 (mol/mol). Intravenous administration of lipid/CAT plasmid complexes resulted in distribution of plasmid DNA mainly to the lung at 15 min after injection. Plasmid DNA accumulation in the liver increased with time up to 24 hr postinjection. There was a 10-fold decrease in the amount of plasmid DNA in the lung at 15 min after injection, when the lipid/plasmid complex charge ratio was decreased from 3:1 to 0.5:1 (+/-). Bright fluorescent aggregates were evident in in vivo-transfected lung with the positively charged pCMV-CAT/DOLCE:dioleyl phosphatidylethanolamine (DOPE) (1:1, mol/mol) complexes, while more discrete punctate fluorescence was observed with a 4:1 molar ratio of cationic lipid:colipid formulations. Preinjection of polyanions such as plasmid, dextran sulfate, polycytidic acid, and polyinosinic acid decreased hGH expression, whereas the preinjection of both positively charged and neutral liposomes had no effect on hGH serum levels. Of the cationic lipids tested, DOLCE was found to be the most effective potentially biodegradable cationic lipid. A correlation between gene expression and cationic lipid:colipid ratios and lipid-to-plasmid charge ratio was also observed for DOTMA- and DOLCE-based formulations.
Optimal Dynamic Pricing of Inventories with Stochastic Demand over Finite Horizons (1994)

In many industries, managers face the problem of selling a given stock of items by a deadline. We investigate the problem of dynamically pricing such inventories when demand is price sensitive and stochastic and the firm's objective is to maximize expected revenues. Examples that fit this framework include retailers selling fashion and seasonal goods and the travel and leisure industry, which markets space such as seats on airline flights, cabins on vacation cruises, and rooms in hotels that become worthless if not sold by a specific time. We formulate this problem using intensity control and obtain structural monotonicity results for the optimal intensity (resp., price) as a function of the stock level and the length of the horizon. For a particular exponential family of demand functions, we find the optimal pricing policy in closed form. For general demand functions, we find an upper bound on the expected revenue based on analyzing the deterministic version of the problem and use this bound to prove that simple, fixed price policies are asymptotically optimal as the volume of expected sales tends to infinity. Finally, we extend our results to the case where demand is compound Poisson; only a finite number of prices is allowed; the demand rate is time varying; holding costs are incurred and cash flows are discounted; the initial stock is a decision variable; and reordering, overbooking, and random cancellations are allowed.
Characterisation of the Local Inflammatory Response in Appendicitis (1993)

Carbohydrate malabsorption after apple juice ingestion may produce abdominal symptoms and diarrhea, especially in children. The carbohydrates suggested to play roles in this process are fructose, as it is present in excess of glucose, and sorbitol. Absorption of the carbohydrates in apple juice was investigated in 17 children and 12 adults by means of the hydrogen breath test. Apple juice was given at a dose of 15 ml/kg body weight, with a maximum of 375 ml. Fructose (0.6 g/kg) and sorbitol (0.06 g/kg), alone and in combination, were administered in amounts similar to their contents in apple juice (fructose as excess over glucose content). Apple juice malabsorption, as judged by a peak breath H2 excretion of > or = 20 ppm, was found in 11 children (65%) and 4 adults (33%). Of those malabsorbing apple juice, 7 of 11 children malabsorbed fructose, 1 of 11 sorbitol, and 4 of 11 the combination; the four adults absorbed all test solutions completely. We could not find an additive effect of sorbitol on breath H2 excretion after fructose ingestion. Peak breath H2 concentrations after apple juice ingestion (mean +/- SEM: 43 +/- 7 ppm) were higher than those with fructose (23 +/- 5 ppm; p < 0.05) or the fructose-sorbitol combination (20 +/- 5 ppm; p < 0.05). Fructose, and not sorbitol, is the sugar responsible for the increase in breath H2 after apple juice consumption and therefore for the diarrhea accompanying excessive apple juice consumption in toddlers.
Epigenetics and Cognitive Aging (2010)

Cognitive decline, especially in memory capacity, is a normal part of aging (1). Indeed, the painful reality is that aging-related cognitive decline likely begins when one is in their late 40s. This deterioration is particularly pronounced in declarative memory—the ability to recall facts and experiences—and has been associated with aberrant changes in gene expression in the brain's hippocampus and frontal lobe. However, the molecular mechanisms underlying these changes in gene regulation are not currently known (2, 3). On page 753 of this issue, Peleg et al. (4) bolster an emerging hypothesis that changes in the epigenetic modification of chromatin in the adult central nervous system drive cognitive decline.
Microbiological and biochemical characterization of spirochetes isolated from the feces of homosexual males (1986)

Spirochetes were isolated from the feces of 11 homosexual males who had diarrhea. The anaerobic organisms were isolated from a selective medium that consisted of Trypticase soy agar supplemented with either 5% horse or human blood, 400 micrograms of spectinomycin per ml, and 5 micrograms of polymyxin B per ml. Nonselective media that permitted good growth of these fastidious organisms were developed, and selected biochemical tests were performed. The tests included carbohydrate utilization, detection of certain enzymes, and determination of volatile fatty-acid end products of metabolism. Two growth patterns were noted on solid media, a haze of growth and production of small colonies. Based on the results of biochemical tests, patterns of preformed enzymes, and volatile fatty-acid production, we believe that the 11 isolates represent a heterogeneous group of spirochetes. The data suggest that the human colon may harbor unique strains of cultivable spirochetes; additional study of the taxonomy of the organisms and assessment of their virulence for humans are needed.
HSV-1 infected cell proteins influence tetracycline-regulated transgene expression (2000)

These results indicate that proteins encoded in the HSV-1 genome, especially the transactivating immediate early gene products (ICP4, ICP27 and ICP0) and the VP16 tegument protein can activate the tetO/ minimal CMV promoter and thereby interfere with the integrity of tetracycline-regulated transgene expression.
Improved fabrication of double-barreled recessed cathode O2 microelectrodes (1987)

Polarographic recessed cathode gold microelectrodes are the preferred type of O2 microelectrode for tissue measurements, but the method originally described for their construction is difficult. An improved method of constructing such electrodes consists of several steps: 1) insertion of a rod made of a special low-melting point alloy into a pulled glass micropipette, 2) heating of the electrode tip as the alloy is pushed toward the tip, 3) beveling, and 4) gold plating the alloy, leaving a recess of the desired length. This method can be used to make single- or double-barreled electrodes in which the O2 barrel is as small as 2-3 micron. The electrodes retain their characteristics for several weeks.
Fluorescent Cytochemical Detection of Estrogen and Progesterone Receptors in Breast Fine-Needle Aspirates (1991)

Estrogen and progesterone receptors were studied in fine-needle aspiration biopsy specimens of 56 patients with primary, recurrent, or metastatic breast carcinoma. The ligands, 17 B-estradiol-6-carboxymethyloxine-bovine serum albumin fluorescein isothiocyanate (FITC-BSA estradiol) and hydroxyprogesterone hemisuccinate bovine serum albumin tetramethyl rhodamine isothiocyanate (TMRITC-BSA progesterone), were used in the fluorescent cytochemical method. The findings obtained from the aspirated cells with the use of the fluorescent cytochemical technique were compared with results obtained from the cell population of the same tumor after removal with the use of both the fluorescent cytochemical technique and the biochemical dextran-coated charcoal (DCC) assay. For the needle aspirates, there was 89% concordance for estrogen receptor and 86% concordance for progesterone receptor between biochemical and cytochemical results. A high degree of correlation was also demonstrated between fine-needle aspirates and imprint preparations with the use of the cytochemical technique. This study suggests that the fluorescent cytochemical technique is an effective tool in assessment of estrogen and progesterone receptor content in fine-needle aspirates of primary and metastatic breast cancer. The fluorescent cytochemical technique can be performed easily at community hospitals and is well suited for specimens of insufficient size for biochemical assay.
Component(s) of Sendai virus that can induce interferon in mouse spleen cells (1983)

To identify the active component of Sendai virus that induces interferon in mouse spleen cells, infectious and noninfectious viruses, envelope particles derived from them, and isolated hemagglutinin-neuraminidase (HN) glycoproteins were examined for interferon induction. The interaction between membranous structures containing Sendai virus HN glycoprotein and the receptors on the cell surface was shown to be sufficient for interferon induction in mouse spleen cells, suggesting that the actual inducer of interferon in mouse spleen cells is the HN glycoprotein of Sendai virus. When mouse spleen cells were stimulated in vitro with Sendai virus grown in eggs or LLC-MK2 cells or with membranous structures containing glycoproteins obtained from these viruses, interferon could be detected in the culture fluid. Furthermore, isolated HN glycoprotein per se could induce interferon in the cells. A linear correlation was found between the titer of interferon induced and the hemagglutinating activity of the membranous structure containing the HN glycoprotein. It was concluded from these findings that HN glycoprotein was the active component of Sendai virus responsible for interferon induction in mouse spleen cells and that viral RNA and F glycoprotein were not required. The results also showed that the interaction between HN glycoprotein and receptors on the cell surface triggered production of type I interferon (IFN-alpha and IFN-beta). Although when Sendai virus was incubated at 56 degrees C for 5 min it lost its hemolytic and hemagglutinating activities, it induced a considerable amount of interferon in the culture fluid of mouse spleen cells. The interferon-inducing ability of heat-inactivated virus could be absorbed with mouse spleen cells but not with sheep erythrocytes or mouse erythrocytes, indicating that the inactivated virus retained ability to bind to mouse lymphoid cells.
Absorbing Set Analysis of LDPC Codes and Read-Channel Quantization in Flash Memory (2012)

High-capacity NAND flash memories achieve high-density by storing more than one bit per cell. Storage systems require extremely low block-error-rates, making powerful error-correcting codes with low-error floors necessary. Low-density parity-check (LDPC) codes are well known to approach the capacity of the additive white Gaussian noise (AWGN) channel, but they often suffer from error floors and require soft information to achieve better performance. This dissertation tackles these two problems.The first part of this dissertation introduces the cycle consistency matrix (CCM) as a powerful analytical tool for characterizing and avoiding absorbing sets in separable circulant-based (SCB) LDPC codes. Each potential absorbing set in an SCB LDPC code has a CCM, and an absorbing set can be present in an SCB LDPC code only if the associated CCM is not full column-rank. Using this novel observation, a new code construction approach selects rows and columns from the SCB mother matrix to systematically and provably eliminate dominant absorbing sets by forcing the associated CCMs to be full column-rank. Simulation results both in software and in hardware demonstrate new codes that have steeper error-floor slopes and provide at least one order of magnitude of improvement in the low FER region. This dissertation also shows how identifying absorbing-set-spectrum equivalence classes within the family of SCB codes with a specified circulant matrix significantly reduces the search space of code matrices with distinct absorbing set spectra. For a specified circulant matrix, SCB codes all share a common mother matrix and thereby retain standard properties of quasi-cyclic LDPC codes such as girth, code structure, and compatibility with existing high-throughput hardware implementations. SCB codes include a wide variety of LDPC codes such as array-based LDPC codes as well as many common quasi-cyclic codes. Hence the CCM approach should find wide application.The second part of this dissertation focuses on coding for flash memory. Traditional flash memories employ simple algebraic codes, such as BCH codes, that can correct a fixed, specified number of errors. This dissertation investigates the application to flash memory of low-density parity-check (LDPC) codes which are well known for their ability to approach capacity in the AWGN channel. We obtain soft information for the LDPC decoder by performing multiple cell reads with distinct word-line voltages. The values of the word-line voltages (also called reference voltages) are optimized by maximizing the mutual information between the input and output of the multiple-read channel. Our results show that using this soft information in the LDPC decoder provides a significant benefit and enables the LDPC code to outperform a BCH code with comparable rate and block length over a range of block error rates. Using the maximum mutual-information (MMI) quantization in the LDPC decoder provides an effective and efficient estimate of the word-line voltages compared to other existing quantization techniques.
Murine red blood cells as efficient carriers of three bacterial antigens for the production of specific and neutralizing antibodies (1991)

Three bacterial toxoids, CRM 197 (mutagenized diphtheria toxin), tetanus toxoid (formaldehyde-treated tetanus toxin), and PT-9K/129G (double mutant of pertussin toxin) were encapsulated within red blood cells (RBCs) of B6D2F1 and Balb/C mice according to a mild procedure based on hypotonic dialysis-isotonic resealing that yielded undamaged RBCs. The toxoid-loaded RBCs were injected intravenously in order to immunize animals and their effects were compared to those of identical amounts (30-95 micrograms per mouse subdivided into multiple injections) of the corresponding free toxoids injected intravenously in saline. Sera from treated mice were collected and tested for titers of specific antibodies against each of the three antigens and also for titers of neutralizing antibodies, i.e., affording protection from toxic effects induced by the corresponding native toxins. In all experiments, significant seroconversion was observed with both immunization systems. Titers of both specific and neutralizing antibodies against CRM 197 and tetanus toxoid were several-fold higher upon immunization with the RBC-encapsulated toxoids, than with the free toxoids. These differences were not due to qualitatively different recognition patterns of antigenic determinants by the two types of sera. Conversely, intravenous immunization with pertussis toxoid either as RBC-encapsulated or as free antigen elicited a comparably high production of specific and of neutralizing antibodies. These data demonstrate that properly engineered RBCs behave as natural carriers and possibly adjuvants for antigens of vaccinal interest.