gebhart/patrepeval huggingface dataset:
Functional analysis of genes responsible for the synthesis of the B-band O antigen of Pseudomonas aeruginosa serotype O6 lipopolysaccharide The GenBank accession number for the sequence reported in this paper is AF035937. (1999)

This study reports the organization of the wbp gene cluster and characterization of a number of genes that are essential for B-band O antigen biosynthesis in the clinically prevalent Pseudomonas aeruginosa serotype 06. Twelve genes were identified that share homology with other LPS and polysaccharide biosynthetic genes. This cluster contains homologues of wzx (encoding the O antigen flippase/translocase) and wzz (which modulates O antigen chain length distribution) genes, typical of a wzy-dependent pathway. However, a complete wzy gene (encoding the O-polymerase) was not found within the cluster. Four biosynthetic genes, wbpO, wbpP, wbpV and wbpM, and four putative glycosyltransferase genes, wbpR, wbpT, wbpU and wbpL, were identified in the cluster. To characterize their roles in LPS biosynthesis, null mutants of wbpO, wbpP, wbpV, wbpL and wbpM were generated using a gene-replacement strategy. Mutations in each of these genes caused deficiency in B-band synthesis. The wbpL mutant was deficient in both A-band and B-band LPS. WbpL(O6) is a bi-functional enzyme which could initiate B-band synthesis through the addition of QuiNAc to undecaprenol phosphate, and A-band synthesis by transferring either a GalNAc or a GlcNAc residue. Another approach used to assign function to the wbp(O6) genes was by complementation analysis. Two genes from Salmonella typhi, wcdA and wcdB, responsible for the synthesis of a homopolymer of GalNAcA called Vi antigen were used in complementation experiments to verify the functions of wbpO and wbpP. wcdA and wcdB restored B-band synthesis in wbpO and wbpP mutants respectively, implying that wbpO and wbpP are involved in UDP-GalNAcA synthesis. Although wbpV has homology to wbpK of the serotype O5 B-band LPS synthesis cluster, complementation analysis using the respective null mutants showed that the genes are not interchangeable. A knockout mutation of wbpN (located downstream of wbpM) did not abrogate LPS synthesis in either 05 or 06; therefore, it has been renamed orf48.5. These results establish the organization of genes involved in P. aeruginosa B-band O antigen synthesis and provide the evidence to assign functions to a number of LPS biosynthetic genes.
Nanocarriers Protecting Toward an Intestinal pre-uptake Metabolism (2017)

Pre-uptake metabolism within the GI tract is responsible for the poor oral bioavailability of numerous drugs. As nanocarriers function as a 'shield', protecting incorporated drugs from enzymatic attack, there is an increasing interest in utilizing them as a tool for overcoming drug degradation. Degradation of carriers resulting in the release of incorporated drugs, mucus permeation, enzyme inhibitory properties and their toxicity are crucial factors that must be taken into account when designing proper nanocarriers. The use of polymer- and lipid-based nanocarriers as protective vehicles are discussed within this review. Lipid-based carriers and novel mucopenetrating particles seem to have a great potential in avoiding metabolizing enzymes. Accordingly, nanocarriers are promising tools for improving the bioavailability of drugs, being sensitive to a pre-uptake metabolism.
Protein complementation assays: Approaches for the in vivo analysis of protein interactions (2009)

The in vivo identification and characterization of protein-protein interactions (PPIs) are essential to understand cellular events in living organisms. In this review, we focus on protein complementation assays (PCAs) that have been developed to detect in vivo protein interactions as well as their modulation or spatial and temporal changes. The uses of PCAs are increasing, spanning different areas such as the study of biochemical networks, screening for protein inhibitors and determination of drug effects. Emphasis is given to approaches that rely on signals of spectroscopic nature (i.e. fluorescence or luminescence), the ones that are more directly related to bioimaging.
Monoclonal Antibody Therapy of B Cell Lymphoma: Signaling Activity on Tumor Cells Appears More Important Than Recruitment of Effectors (1998)

Despite the recent success of mAb in the treatment of certain malignancies, there is still considerable uncertainty about the mechanism of action of anti-cancer Abs. Here, a panel of rat anti-mouse B cell mAb, including Ab directed at surface IgM Id, CD19, CD22, CD40, CD74, and MHC class II, has been investigated in the treatment of two syngeneic mouse B cell lymphomas, BCL1 and A31. Only three mAb were therapeutically active in vivo, anti-Id, anti-CD19, and anti-CD40. mAb to the other Ags showed little or no therapeutic activity in either model despite giving good levels of surface binding and activity in Ag-dependent cellular cytotoxicity and complement assays, and in some cases inhibiting cell growth in vitro. We conclude that the activity of mAb in vitro does not predict therapeutic performance in vivo. Furthermore, in vivo tracking experiments using fluorescently tagged cells showed that anti-Id and anti-CD40 mAb probably operate via different mechanisms: the anti-Id mAb cause growth arrest that is almost immediate and does not eliminate cells over a period of 5 or 6 days, and the anti-CD40 mAb have a delayed effect that allows tumor to grow normally for 3 days, but then abruptly eradicates lymphoma cells. This work supports the belief that mAb specificity is critical to therapeutic success in lymphoma and that, in addition to any effector-recruiting activity they may possess, in vivo mAb operate via mechanisms that involve cross-linking and signaling of key cellular receptors.
Interactive methods for visualizable geometry (1994)

Interactive computer graphics can provide new insights into the objects of pure geometry, providing intuitively useful images, and, in some cases, unexpected results. Interactive computer graphics systems have opened a new era in the visualization of pure geometry. We demonstrate the fruitful relationship between mathematics and the discipline of computer graphics, emphasizing those areas of low-dimensional geometry and topology where interactive paradigms are of growing importance.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A quantitative scale to define endoscopic torque control during natural orifice surgery (2012)

Pattern of movements extrapolated from the wrist can be used as a method of measuring endoscope torque control during a translumenal navigation task.
Estimate of the Mutation Rate per Nucleotide in Humans (2000)

Many previous estimates of the mutation rate in humans have relied on screens of visible mutants. We investigated the rate and pattern of mutations at the nucleotide level by comparing pseudogenes in humans and chimpanzees to (i) provide an estimate of the average mutation rate per nucleotide, (ii) assess heterogeneity of mutation rate at different sites and for different types of mutations, (iii) test the hypothesis that the X chromosome has a lower mutation rate than autosomes, and (iv) estimate the deleterious mutation rate. Eighteen processed pseudogenes were sequenced, including 12 on autosomes and 6 on the X chromosome. The average mutation rate was estimated to be approximately 2.5 x 10(-8) mutations per nucleotide site or 175 mutations per diploid genome per generation. Rates of mutation for both transitions and transversions at CpG dinucleotides are one order of magnitude higher than mutation rates at other sites. Single nucleotide substitutions are 10 times more frequent than length mutations. Comparison of rates of evolution for X-linked and autosomal pseudogenes suggests that the male mutation rate is 4 times the female mutation rate, but provides no evidence for a reduction in mutation rate that is specific to the X chromosome. Using conservative calculations of the proportion of the genome subject to purifying selection, we estimate that the genomic deleterious mutation rate (U) is at least 3. This high rate is difficult to reconcile with multiplicative fitness effects of individual mutations and suggests that synergistic epistasis among harmful mutations may be common.
Surface-Enhanced Raman Spectroscopy (2008)

The ability to control the size, shape, and material of a surface has reinvigorated the field of surface-enhanced Raman spectroscopy (SERS). Because excitation of the localized surface plasmon resonance of a nanostructured surface or nanoparticle lies at the heart of SERS, the ability to reliably control the surface characteristics has taken SERS from an interesting surface phenomenon to a rapidly developing analytical tool. This article first explains many fundamental features of SERS and then describes the use of nanosphere lithography for the fabrication of highly reproducible and robust SERS substrates. In particular, we review metal film over nanosphere surfaces as excellent candidates for several experiments that were once impossible with more primitive SERS substrates (e.g., metal island films). The article also describes progress in applying SERS to the detection of chemical warfare agents and several biological molecules.
Interdependencies of Electricity Market Characteristics and Bidding Strategies of Power Producers (2002)

In the context of the ongoing deregulation of the electricity industry, we revisit the commonly held assumption that, under the condition of perfect information, a decentralized unit commitment would lead to the same power quantities traded and the same optimal social welfare as centralized unit commitment. Taking fixed operating costs into account, we show that meeting decentralized performance objectives of the individual market participants can lead to a lower efficiency than minimizing total operating cost in a decentralized way. This result concerns short-term optimization, and does not consider long-term investment issues. Next, the task of optimally self-scheduling generators to maximize profits in a
Clinical implications of increased expression of CD40L in patients with acute coronary syndromes. (2002)

Enhanced level of serum sCD40L may be a reliable prognostic indicator for ACS and may represent a marker of coronary disease activity.
m (2010)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Wiring space and length estimation in two-dimensional arrays (2000)

We propose a new global routing area estimation approach for high-performance very large scale integration and multichip modules (MCMs). The objective is to route nets with minimum density of global cells, producing a four-bend routing for each two-terminal net. We propose an approximate upper bound on global cell d/sub H//spl les/2d/sub 0/log(m/(2d/sub 0/)), in an m/spl times/m two-dimensional array, where d/sub 0/ is the estimated lower-bound density. The total wirelength is (2/spl alpha/+/spl beta/)4m/sup 2/d/sub 0//3, where /spl alpha/+/spl beta/=1 and /spl alpha/ is the percentage of diagonal combinations and /spl beta/ is the percentage of adjacent combinations of nets. If /spl alpha//spl les//spl beta/ (this assumption holds since a good placement minimizes the longer wires), then the total wirelength is at most 2m/sup 2/d/sub 0/. By counting on the adjacent and diagonal combinations separately in the cost function, d/sub R//spl les/[4d/sub 0//3]/spl times/log([m/(4d/sub 0//3)]). We verified that the bound obtained are realistic in the worst case. A solution to this problem can be used for quick estimation of necessary wiring space (for standard cell array designs) and difficulty of routing (for gate array designs) in the early design planning stage.
Interleukin 1 induces expression of the human immunodeficiency virus alone and in synergy with interleukin 6 in chronically infected U1 cells: inhibition of inductive effects by the interleukin 1 receptor antagonist. (1994)

In the present study we have observed that interleukin (IL) 1 alpha or IL-1 beta directly induced expression of human immunodeficiency virus (HIV) in the latently infected human promonocytic cell line U1. In addition, IL-1 synergized with IL-6, but not with tumor necrosis factor, in the upregulation of virus expression in U1 cells as measured by accumulation of steady-state mRNAs and production of reverse transcriptase activity. The HIV inductive effect of IL-1 was blocked by transforming growth factor beta, anti-IL-1 antibodies, or monoclonal antibodies directed to the type 1, but not to the type 2, cell surface receptor for IL-1; the latter actually caused enhancement of the IL-1-mediated effect. Unlike tumor necrosis factor alpha, IL-1 either alone or in combination with IL-6 did not induce activation of the transcription activating factor NF-kappa B above the constitutive levels of unstimulated U1 cells. Finally, the IL-1 receptor antagonist effectively blocked IL-1-mediated direct and synergistic inductive effects on virus production. Thus, IL-1 may be an important mediator of HIV expression, and blocking of IL-1 expression and/or its effects may have a potential therapeutic role in the inhibition of HIV expression in infected individuals.
The Hypothalamic–Pituitary–Adrenal Axis and Immune-Mediated Inflammation (1995)

Celsus described four of the five cardinal signs of inflammation 2000 years ago, and Eustachio discovered the adrenal glands almost 500 years ago, but not until 1936 did Selye note that in rats exposed to stressors, the adrenal glands were enlarged, and the thymus and lymph nodes shrunken.13 Cortisone, the active principle of the adrenal glands, was isolated by Kendall and Reichstein in the late 1940s and shown to suppress immune organs. These scientists, along with Hench, received the Nobel Prize in Physiology and Medicine, after Hench and colleagues showed that cortisone could ameliorate rheumatoid arthritis.4,5 In recent . . .
CD69 in resting and activated T lymphocytes. Its association with a GTP binding protein and biochemical requirements for its expression (1991)

CD69 is a phosphorylated disulfide-linked homodimer that appears on the surface of human T, B cells and thymocytes in the early steps of activation; its molecular mass is 28 to 34 kDa under reducing conditions. This molecule is able to mediate positive signals to the lymphocytes as the anti-CD69 mAb (MLR3, AIM, Leu 23) in synergism with phorbol esters induce IL-2 production and proliferation of lymphocytes. Here we show that this molecule is associated to a GTP binding protein that is a substrate for Bordetella pertussis toxin. The relevance of CD69 in the activation process is also suggested by the broad range of signals able to modulate CD69 on T cells. In fact, not only the mitogens or the CD3-promoted activation, but also the alternative pathways mediated by CD2 or CD28 are accompanied by CD69 expression; moreover a very rapid and transient appearance of CD69 on the cell surface is observed also in response to a stimulus not specifically involved in T cell activation such as heat shock. Finally we demonstrate that CD69 is present in the cytoplasm of nonactivated T cells; accordingly its surface expression at the onset of activation is independent on a new RNA or protein synthesis.
Inhibition of cell proliferation of human gliomas by benzodiazepinesin vitro (1988)

The effects of several benzodiazepines (diazepam, clonazepam, Ro 15-1788 and Ro 5-4864) on cell proliferation of 2 human gliomas were estimated in vitro by means of [3H]-thymidine uptake assay. It was found that all tested benzodiazepines suppressed [3H]-thymidine incorporation into the DNA of glioma cells, the effects being stronger in case of peripheral-type benzodiazepine receptor ligands. The results indicated that benzodiazepines might exert an antiproliferative action on glioma tumour cells growth.
Phenotypic Trends in Incidence of Stillbirth for Holsteins in the United States (2001)

The objectives for this study were to determine 1) if there was a trend in stillbirths for the U.S. Holstein population, 2) if stillbirths are the same trait in primiparous and multiparous cows, and 3) what was the role of dystocia in stillbirths. A sample of 666,341 births from the MidStates Dairy Records Processing Center and the National Association of Animal Breeders was used to examine the influence of sire, herd, year, season, sex of calf, parity of dam, calving ease, and gestation length on the survival of the calf. Parity was scored as an ordered variable (1, 2, 3+). Calving ease was scored on a scale of 1 (no assistance) to 3+ (needed assistance). An increasing trend in stillbirths was found in primiparous and multiparous cows. The percentage of stillborn calves in primiparous cows increased from 9.5 in 1985 to 13.2 in 1996. Stillbirths in multiparous cows increased from 5.0 to 6.6% from 1985 to 1996. Variation about the trend was greater in primiparous cows than in multiparous cows. Dystocia was a major determinant of stillbirth incidence, but the association was stronger in primiparous cows. Sex of calf had different associations with stillbirth incidence in primiparous and multiparous cows. Gestation length and season of birth also had significant associations with stillbirth incidence. Logistic regression models with fixed and random effects were fit to the data to preserve the binary nature of the stillbirth response. The expected probability of stillbirths for an average herd and sire was 10% for primiparous cows and 5% for multiparous cows. Replacement of stillborn calves is a substantial cost to the dairy industry at more than $125.3 million per year. Because of the increasing incidence of stillbirths, these costs have increased by $75.9 million from 1985 to 1996.
Induction of Anti-Phospholipid Autoantibodies by β2-glycoprotein I Bound to Apoptotic Thymocytes (1998)

The target of many anti-phospholipid autoantibodies (aPL) has been shown to be a complex between anionic phospholipid and the plasma protein beta2-glycoprotein I (beta2GPI) or the protein beta2GPI alone. As aPL binding studies have been performed almost exclusively in vitrothe identity of the natural target and/or immunogen for aPL in vivo remains undetermined. The anionic phospholipids of cell membranes represent an important potential target and immunogen for aPL. Although anionic phospholipids are normally absent from the extracellular surface of cell membranes, they redistribute from the inner to the outer leaflet during apoptosis. We have previously shown that beta2GPI binds selectively to the surface of apoptotic, but not viable, cells, and that binding of beta2GPI to the surface of apoptotic cells generates an epitope recognized by aPL from patients with primary aPL syndrome and systemic lupus erythematosus. We show here that immunization of non-autoimmune mice with beta2GPI combined with, or bound to, apoptotic cells induces aPL and lupus anticoagulant activity. Generation of aPL required heterologous beta2GPI, and occurred upon immunization with apoptotic cells and beta2GPI by three different routes of administration. Importantly, for intravenous immuniz-ations, generation of aPL occurred only when apoptotic cells and beta2GPI were injected together, but not when either was injected alone, suggesting that cell-bound beta2GPI is the true immunogen for production of aPL. Unlike other models of induced aPL, adjuvant was not an absolute requirement. Induced aPL reacted with murine, as well as bovine, beta2GPI, suggesting that heterologous beta2GPI bound to apoptotic cells can break tolerance and induce auto-antibodies reactive with autologous beta2GPI. Combined with our previous data, these results show that apoptotic cells can serve as both immunogens and natural targets for aPL.
Expression of B7-H1 in Inflammatory Renal Tubular Epithelial Cells (2005)

This study clearly shows that B7-H1 is an inducible renal tubular epithelial antigen that inhibits T cell activation. It is speculated that B7-H1/PD-1 pathway might play a role in protecting tubular epithelium from immune-mediated damage and active delivery of the B7-H1 inhibitory signal represents a novel therapeutic strategy in autoimmune renal diseases.
Multiparametric sensor-chip based technology for monitoring metabolic activity: A proof-of-principle study with live tissue. (2006)

The recent development of an electronic test system based on silicon sensor-chips allows the continuous parallel recording of relative changes in extracellular acidification, oxygen consumption and electric impedance in living cells. The objective of this proof-of-principle study therefore, was to clarify whether this system can also be applied to live tissue slices thus providing a device for an ultimately envisioned chemosensitivity testing apparatus for individualized treatment schemes in cancer therapy. A prototype of the testing apparatus equipped with six individual measuring devices has been used to simultaneously analyze changes in extracellular acidification, oxygen consumption and electronic impedance in live liver tissue and compared to data obtained from a tumor cell line. In contrast to tumor cells, tissue slices showed low rates of extracellular acidification but high rates of oxygen consumption. Monitoring of electrical impedance values, reflecting cellular morphology, revealed that the compact cell structure of the tissue slices was able to function as electric insulator and actively change the impedance values of the system. Exposure of tumor cells to 1 microM cytochalasin B, a fungal metabolite known to interact with the cytoskeleton and influence glucose metabolism, resulted in the rapid decline of extracellular acidification, increased oxygen consumption rates and increased values in capacitance. In tissue slices upon addition of 1 microM cytochalasin B, a decline of both extracellular acidification and electrical impedance was observed within 1 h. Determination of ATP content in the tissue slices revealed that decreasing ATP content paralleled diminishing oxygen consumption. This new technique offers the possibility of generating metabolic profiles for cells and tissues by studying oxygen consumption, extracellular acidification and electrical impedance.
Antibody-Directed Urokinase: A Specific Fibrinolytic Agent (1985)

A specific fibrinolytic agent was synthesized by covalently coupling urokinase to a monoclonal antibody that was fibrin-specific and did not cross-react with fibrinogen. The antibody was raised against a synthetic peptide representing the seven amino-terminal residues of the beta chain of human fibrin. The urokinase-antifibrin conjugate retained the original binding specificity of the antibody and showed 100-fold increased fibrinolysis in vitro when compared to unmodified urokinase. The presence of human fibrinogen at plasma concentration did not influence these properties.