gebhart/patrepeval huggingface dataset:
Planning feeder links to broadcasting satellites (1984)

This paper discusses the planning of feeder links to broadcasting satellites, including consideration of the parameters, performance measures and interference criteria applicable to them. The concepts of satellite clustering, power control and depolarization compensation and site diversity are discussed. Simultaneous planning of feeder links and down-links is contrasted with the independent planning of those links
Interleukin‐1 and Tumor Necrosis Factor‐α Inhibit Erythropoietin Production in Vitroa (1991)

The effects of several immunomodulatory peptides (recombinant, human) on the in vitro production of erythropoietin (Epo) were studied in cultures of the human hepatoma cell line Hep G2. A dose-dependent decrease of up to 60% in Epo production was induced by interleukin-1 beta, interleukin-1 alpha, and tumor necrosis factor-alpha (in that order of potency). In contrast, moderately increased Epo levels resulted with interleukin-6 or interferon-gamma treatment at high concentrations. Concomitant measurements of the production of alpha-fetoprotein indicated that the observed effects were specific for Epo. Hence, we suspect a modulating role of the immune system in the in vivo control of Epo production and postulate that interleukin-1 and tumor necrosis factor-alpha are involved in some of the cases of lowered blood Epo levels in association with renal diseases, chronic inflammation, and malignancies.
MethylQuant: a sensitive method for quantifying methylation of specific cytosines within the genome (2004)

Here we present MethylQuant, a novel method that allows accurate quantification of the methylation level of a specific cytosine within a complex genome. This method relies on the well-established treatment of genomic DNA with sodium bisulfite, which converts cytosine into uracil without modifying 5-methyl cytosine. The region of interest is then PCR-amplified and quantification of the methylation status of a specific cytosine is performed by methylation-specific real-time PCR with SYBR Green I using one of the primers whose 3' end discriminates between the methylation states of this cytosine. The presence of a locked nucleic acid at the 3' end of the discriminative primer provides the specificity necessary for accurate and sensitive quantification, even when one of the methylation states is present at a level as low as 1% of the overall population. We demonstrate that accurate quantification of the methylation status of specific cytosines can be achieved in biological samples. The method is high-throughput, cost-effective, relatively simple and does not require any specific equipment other than a real-time PCR instrument.
Transcriptional activation by the PHD finger is inhibited through an adjacent leucine zipper that binds 14-3-3 proteins (2000)

The PHD finger, a Cys(4)-His-Cys(3) zinc finger, is found in many regulatory proteins from plants or animals which are frequently associated with chromatin-mediated transcriptional regulation. We show here that the PHD finger activates transcription in yeast, plant and animal cells. In plant homeodomain transcription factors the PHD finger is combined with an upstream leucine zipper. Both domains together form a highly conserved 180 amino acid region called the ZIP/PHDf motif and transcriptional activity of the PHD finger is masked when embedded in this motif. Our results indicate that the ZIP/PHDf domain is a potential regulatory domain of PHDf-HD proteins. The leucine zipper upstream of the PHD finger interacts with 14-3-3GF14 mu from Arabidopsis thaliana and 14-3-3GF14-12 from maize via a leucine zipper conserved in helix 4 of various 14-3-3 proteins from plants and animals. PHD-type plant homeodomain proteins consequently may represent potential targets of 14-3-3 signalling.
Conformation-selective DNA strand breaks by dynemicin: A molecular wedge into flexible regions of DNA (1993)

We present evidence that the enediyne antitumor antibiotic dynemicin recognizes and cleaves conformationally flexible regions of DNA. This is based on specific strand breaks at mismatches, bulges, and nicks as determined by high-resolution sequencing gels. On the basis of the weak association constant of dynemicin for DNA, it is expected that these more flexible regions would be preferred sites. In addition, the DNA unwinding behavior of dynemicin and the absorption spectrum of the dynemicin-DNA complex are strongly indicative of its intercalative binding with DNA. The results allow us to propose dynemicin as a molecular wedge that binds to the DNA by intercalating into the minor-groove side of conformationally flexible regions of DNA. Presumably, DNA local flexibility is able to create an open pocket in the minor groove, permits facile intercalation of dynemicin, and then increases the chances of its DNA damaging event. Implications for the biological action of dynemicin have also been discussed.
The same exhaustible multilineage precursor produces both myeloid and lymphoid cells as early as 3-4 weeks after marrow transplantation. (1992)

Hemopoietic precursors with the ability to differentiate into wide varieties of cell types are considered primitive, as are precursors with long-term repopulating ability. Here we study the populations of marrow precursors from which both myeloid and lymphoid lineages are descended shortly after transplantation. Surprisingly, few or none of these precursors show long-term repopulating ability. Equal portions of a mixture of marrow cells from C57BL/6J (B6) and congenic B6-Hbbd Gpi-1a mice are transplanted into a group of recipients. Three weeks later, highly significant correlations between percentages of B6 type T cells, B cells, granulocytes, and platelets in each recipient indicate that many lymphoid and myeloid cells are descended from common precursors. After 4-6 weeks, most correlations between lymphoid and myeloid cells improve, indicating that most or all differentiated cells are descended from common precursors. The more differentiated myeloid-specific precursors found in spleen colony-forming cell assays apparently fail to contribute significantly to the differentiated myeloid cell populations tested. By using the binomial model, in which variability of the data among the recipients is inversely related to the number of precursors in the mixture, donor precursor concentrations are estimated as approximately 21 per 10(5) marrow cells after 3 weeks, falling 3-fold to 6.6 per 10(5) after 4-6 weeks. This trend continues, with higher correlations, greater variabilities, and donor precursor concentrations of 1.9 per 10(5) marrow cells after 12-14 weeks and 1.4 per 10(5) after 24 weeks. Strong increases in variances between 3 and 12 weeks after transplantation suggest that most or all of the initially active multilineage precursors are exhausted during this time period. The fact that the ability of a hemopoietic stem cell to differentiate into widely disparate lineages is not associated with long-term repopulating ability requires a change in stem cell definitions, since primitive hemopoietic stem cells have traditionally been defined by both these abilities.
Antigenicity and immunogenicity of Melan‐A/MART‐1 derived peptides as targets for tumor reactive CTL in human melanoma (2002)

Some cancer patients mount spontaneous T- and B-cell responses against their tumor cells. Autologous tumor reactive CD8 cytolytic T lymphocyte (CTL) and CD4 T-cell clones as well as antibodies from these patients have been used for the identification of genes encoding the target antigens. This knowledge opened the way for new approaches to the immunotherapy of cancer. In this review, we describe the characterization of the structure-function properties of the melanocyte/melanoma tumor antigen Melan-A/MART-1, the assessment of the T-cell repertoire available against this antigen in healthy individuals, and the analysis of naturally acquired and/or vaccine-induced CTL responses to this antigen in patients with metastatic melanoma.
Artificial Neural Networks (2005)

Abstract Artificial neural networks are useful tools that have been applied successfully in a broad range of signal‐processing problems. From a signal‐processing perspective, their ability to adapt continuously to new data allows them to track changes in a signal over time, and their ability to learn from arbitrary, noisy data permits them to solve problems that cannot be handled adequately with some of the conventional statistical techniques. This chapter presents the fundamental principles of neural network modeling and illustrates some of the most commonly used neural network architectures for practical problem solving.
Bacterial Modulation of Plant Ethylene Levels (2015)

A focus on the mechanisms by which ACC deaminase-containing bacteria facilitate plant growth.Bacteria that produce the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase, when present either on the surface of plant roots (rhizospheric) or within plant tissues (endophytic), play an active role in modulating ethylene levels in plants. This enzyme activity facilitates plant growth especially in the presence of various environmental stresses. Thus, plant growth-promoting bacteria that express ACC deaminase activity protect plants from growth inhibition by flooding and anoxia, drought, high salt, the presence of fungal and bacterial pathogens, nematodes, and the presence of metals and organic contaminants. Bacteria that express ACC deaminase activity also decrease the rate of flower wilting, promote the rooting of cuttings, and facilitate the nodulation of legumes. Here, the mechanisms behind bacterial ACC deaminase facilitation of plant growth and development are discussed, and numerous examples of the use of bacteria with this activity are summarized.
Glucokinase Overexpression Restores Glucose Utilization and Storage in Cultured Hepatocytes from Male Zucker Diabetic Fatty Rats (1999)

Zucker diabetic fatty rats develop type 2 diabetes concomitantly with peripheral insulin resistance. Hepatocytes from these rats and their control lean counterparts have been cultured, and a number of key parameters of glucose metabolism have been determined. Glucokinase activity was 4.5-fold lower in hepatocytes from diabetic rats than in hepatocytes from healthy ones. In contrast, hexokinase activity was about 2-fold higher in hepatocytes from diabetic animals than in healthy ones. Glucose-6-phosphatase activity was not significantly different. Despite the altered ratios of glucokinase to hexokinase activity, intracellular glucose 6-phosphate concentrations were similar in the two types of cells when they where incubated with 1-25 mM glucose. However, glycogen levels and glycogen synthase activity ratio were lower in hepatocytes from diabetic animals. Total pyruvate kinase activity and its activity ratio as well as fructose 2,6-bisphosphate concentration and lactate production were also lower in cells from diabetic animals. All of these data indicate that glucose metabolism is clearly impaired in hepatocytes from Zucker diabetic fatty rats. Glucokinase overexpression using adenovirus restored glucose metabolism in diabetic hepatocytes. In glucokinase-overexpressing cells, glucose 6-phosphate levels increased. Moreover, glycogen deposition was greatly enhanced due to the activation of glycogen synthase. Pyruvate kinase was also activated, and fructose-2,6-bisphosphate concentration and lactate production were increased in glucokinase-overexpressing diabetic hepatocytes. Overexpression of hexokinase I did not increase glycogen deposition. In conclusion, hepatocytes from Zucker diabetic fatty rats showed depressed glycogen and glycolytic metabolism, but glucokinase overexpression improved their glucose utilization and storage.
Cloning of the mouse agouti gene predicts a secreted protein ubiquitously expressed in mice carrying the lethal yellow mutation. (1993)

The mouse agouti gene controls the deposition of yellow and black pigment in developing hairs. Several dominant alleles, including lethal yellow (Ay), result in the exclusive production of yellow pigment and have pleiotropic effects that include obesity and increased tumor susceptibility. In an interspecific backcross, we established genetic limits for the agouti gene and found that the Ay and the lethal non-agouti (ax) allele were not separated from a previously identified probe at the breakpoint of the Is1GsO chromosomal rearrangement. Using the Is1GsO probe, we isolated the agouti gene, and find that it has the potential to code for a secreted protein expressed in hair follicles and the epidermis, and that the level of expression correlates with the synthesis of yellow pigment. In the Ay mutation, there is a chromosomal rearrangement that results in the production of a chimeric RNA expressed in nearly every tissue of the body. The 5' portion of this chimeric RNA contains highly expressed novel 5' sequences, but the 3' portion retains the protein-coding potential of the nonmutant allele. We speculate that dominant pleiotropic effects of Ay are caused by ectopic activation of a signaling pathway similar to that used during normal hair growth.
The Effect of Intranasal Cocaine and Lidocaine on Nitroglycerin‐Induced Attacks in Cluster Headache (2000)

The administration of nitroderivatives in cluster headache (CH) sufferers is the most reproducible experimental paradigm to induce spontaneous-like pain attacks. Previous uncontrolled studies have reported that the local use of anaesthetic agents in the area of the sphenopalatine fossa is able to extinguish nitroglycerin (NTG)-induced pain in CH. The present study, carried out according to a double-blind placebo-controlled design, included 15 CH patients, six with episodic CH (mean +/- SD age of 36.8+/-5.6 years), and nine with chronic CH (37.8+/-10.4 years). Patients had undergone a standard NTG test (0.9 mg sublingually), during which the intensity of pain was scored using a visuoanalogic scale (VAS, range 0-10). Nine patients (two with the episodic form, seven with the chronic form) experienced a typical, spontaneous-like attack on the usual side, occurring in all cases within 45 min. In these patients, the test was repeated with an interval of 2 days, and once pain intensity reached 5 on the VAS, a 10% solution of cocaine hydrochloride (1 ml, mean amount per application 40-50 mg), or 10% lidocaine (1 ml), or saline was applied using a cotton swab in the area corresponding to the sphenopalatine fossa, under anterior rhinoscopy. This was done in both the symptomatic and the non-symptomatic side, for 5 min. Treatments were always performed randomly, in separate sessions. All patients responded promptly to both anaesthetic agents, with complete cessation of induced pain occurring after 31.3+/-13.1 min for cocaine and 37.0+/-7.8 min for lidocaine (M+/-SD). In the case of saline application, pain severity increased thereafter, and extinction of the provoked attacks occurred with a latency of 59.3+/-12.3 min (P<0.01 and P<0.01 vs. cocaine and lidocaine, respectively, Mann-Whitney U-test). While further suggesting that the sphenopalatine ganglion participates in the mechanisms of pain, these findings indicate that the local administration of the anaesthetic agents cocaine and lidocaine is effective on NTG-induced CH attacks, and may be used in the symptomatic treatment of this disorder.
Developing G-quartet oligonucleotides as novel anti-HIV agents: focus on anti-HIV drug design (2000)

Recently, a new class of oligonucleotides, forming G-quartet structures, has been developed as novel anti-HIV agents. Several critical structure-activity relationships between HIV-1 integrase and G-quartet oligonucleotides have been demonstrated. In addition the mechanism of the inhibition of HIV-1 integrase by G-quartet oligonucleotides, such as T30695 and its derivatives, has been explored. This review summarises the preliminary studies of developing G-quartet oligonucleotides as novel anti-HIV agents in several aspects including structure-activity relationship, stability-activity correlation, mechanism of HIV-1 integrase inhibition, substitution of phosphorothioates and targeting HIV-1 integrase in infected cells, which, hopefully, could help for developing a novel, efficient anti-HIV agent.
Effect of different microstructures of e‐PTFE membranes on bone regeneration and soft tissue response: a histologic study in canine mandible (1999)

The purpose of the present study was to compare the effect of 3 types of titanium reinforced e-PTFE membranes (GTRM #1, #2, and #3) on bone regeneration and tissue integration. GTRM #1 was a standard titanium reinforced membrane, GTRM #2 was a prototype characterized by a more open total surface microstructure and GTRM #3 was a prototype characterized by two extremely porous external layers separated by a totally occlusive internal layer. The membranes were used to cover saddle type ridge defects surgically created in the mandible of 6 dogs. After a healing period of 6 months, all the membrane protected sites demonstrated almost complete osseous healing of the defects. GTRM #3 specimens showed the most favourable biologic response, in fact they were characterized by a larger surface of contact between the membrane and the regenerated bone, but from a clinical point of view GTRM #3 material was too difficult to remove. The results of this study suggest that an extremely open porous microstructure, in combination with a totally occlusive barrier, may provide significant improvements in regenerative outcomes. However, these design characteristics may be applied only to resorbable devices, which do not require removal.
The role of complement in kidney disease (2020)

While the complement cascade is an important component of the innate immune system, uncontrolled activation can cause severe disease. This concept is illustrated by the prototypical complement-mediated renal disease atypical haemolytic uraemic syndrome (aHUS), which causes renal failure if untreated but when managed with the complement inhibitor eculizumab leaves the patient vulnerable to infection with encapsulated organisms. Complement activation is also implicated in the pathogenesis of many other renal and non-renal diseases, necessitating an understanding of complement biology and diagnostics. We review renal diseases in which complement over-activation is known to cause tissue injury; aHUS and C3 glomerulopathy. We also discuss the contribution of complement more widely to the pathophysiology of renal disease, and highlight the significance and side effects of anti-complement therapy relevant to the general physician.
Novel ATP-Competitive Kinesin Spindle Protein Inhibitors (2007)

Kinesin spindle protein (KSP), an ATPase responsible for spindle pole separation during mitosis that is present only in proliferating cells, has become a novel and attractive anticancer target with potential for reduced side effects compared to currently available therapies. We report herein the discovery of the first known ATP-competitive inhibitors of KSP, which display a unique activity profile as compared to the known loop 5 (L5) allosteric KSP inhibitors that are currently under clinical evaluation. Optimization of this series led to the identification of biphenyl sulfamide 20, a potent KSP inhibitor with in vitro antiproliferative activity against human cells with either wild-type KSP (HCT116) or mutant KSP (HCT116 D130V). In a murine xenograft model with HCT116 D130V tumors, 20 showed significant antitumor activity following intraperitoneal dosing, providing in vivo proof-of-principle of the efficacy of an ATP-competitive KSP inhibitor versus tumors that are resistant to the other known KSP inhibitors.
Expression cloning of human and rat renal cortex Na/Pi cotransport. (1993)

We have isolated two cDNA clones, NaPi-2 and NaPi-3, by screening rat kidney cortex and human kidney cortex cDNA libraries, respectively, for expression of sodium-dependent phosphate transport in Xenopus laevis oocytes. Substrate specificity and a detailed kinetic analysis (Na, Pi, H+ concentrations) suggested that expressed uptake activities relate to proximal tubular brush border membrane Na/Pi cotransport. NaPi-2 cDNA contains 2464 bp encoding a protein of 637 aa; NaPi-3 cDNA contains 2573 bp encoding a protein of 639 aa. NaPi-2- and NaPi-3-deduced protein sequences show high homology to each other but are different from the protein sequence deduced from the previously cloned NaPi-1 cDNA (from rabbit proximal tubules). Hydropathy profile predictions suggest at least eight membrane-spanning regions in NaPi-2/3-related proteins. In vitro translation results in proteins of the expected size and suggests glycosylation. Northern blot analysis shows corresponding mRNA species (approximately 2.7 kb) in kidney cortex of various species but no hybridization with RNAs isolated from a variety of other tissues (including intestinal segments); a hybridization signal (approximately 4.8 kb) was observed only in the lung (human). We conclude that we have structurally identified two closely related proteins most likely involved in human and rat renal brush border Na/Pi cotransport.
Definition of antigenic heterogeneity and modulation among human mammary carcinoma cell populations using monoclonal antibodies to tumor-associated antigens. (1983)

Murine monoclonal antibodies, prepared against human metastatic mammary tumor cells, were used to demonstrate differential expression of several tumor-associated antigens (TAAs) among various mammary carcinomas and within a given tumor mass. Using the immunoperoxidase technique on serial sections of 39 human primary mammary carcinomas, a spectrum of antigenic phenotypes of TAAs was observed: 13% of the tumors reacted with all of a panel of four monoclonal antibodies; while 10% of the mammary tumors scored negative with all four antibodies. The remaining 30 tumors could be divided into several additional groups based on their differential reactivity with some, but not all, of the monoclonal antibodies. Furthermore, variation among mammary carcinomas was also observed in the cellular localization of antigens. Antigenic phenotypic diversity of mammary tumor cell populations within a given tumor mass was also observed; this was noted with respect to (a) antigenic expression in one area of a tumor mass and not another and (b) a "patchwork" effect in which antigens were expressed on cells immediately adjacent to cells which scored negative. Antigenic phenotypic diversity was also observed in established mammary tumor cell lines grown in vitro. A differential loss of some cell surface TAAs was observed as a function of continued cell passage; consistent with this finding, MCF-7 mammary tumor cell lines obtained from four sources could be differentiated from each other by their pattern of cell surface TAA expression. Single-cell clones derived from the MCF-7 mammary tumor cell line exhibited at least four distinct antigenic phenotypes; a change in cell surface phenotype of some of the clones was seen during subsequent passage. This definition of phenotypic variation and modulation of TAA expression among, and within, human mammary carcinomas has implications towards both the design and the outcome of studies involving the in situ immunodetection and therapy of breast cancer.
Purpose based access control of complex data for privacy protection (2005)

As privacy becomes a major concern for both consumers and enterprises, many research efforts have been devoted to the development of privacy protecting technology. We recently proposed a privacy preserving access control model for relational databases,where purpose information associated with a given data element specifies the intended use of the data element. In this paper, we extend our previous work to handle other advanced data managementsystems, such as the ones based on XML and the ones based on the object-relational data model. Another contribution of our paper isthat we address the problem of how to determine the purpose forwhich certain data are accessed by a given user. Our proposedsolution relies on the well-known RBAC model as well as the notionof conditional role which is based on the notions of role attributeand system attribute.