gebhart/patrepeval huggingface dataset:
Causal Diagrams for Epidemiologic Research (1999)

Causal diagrams have a long history of informal use and, more recently, have undergone formal development for applications in expert systems and robotics. We provide an introduction to these developments and their use in epidemiologic research. Causal diagrams can provide a starting point for identifying variables that must be measured and controlled to obtain unconfounded effect estimates. They also provide a method for critical evaluation of traditional epidemiologic criteria for confounding. In particular, they reveal certain heretofore unnoticed shortcomings of those criteria when used in considering multiple potential confounders. We show how to modify the traditional criteria to correct those shortcomings. (Epidemiology 1999;10:37–48)
Fast mixing by lamination (2002)

A micro mixer based on multi-stage multi-layer lamination is presented. The micro mixer has been designed as an integrated part of a micromachined chemical analysis system. The fabrication technology is based on wet chemical etching of PYREX-glass and silicon substrates which are subsequently bonded anodically. The micro mixer is designed to work in the flow range 1-10 /spl mu/l/min with a Reynolds number less than 1 and an undisturbed laminal flow pattern. Comprehensive theoretical studies and computer simulations have been carried out in order to understand the detailed flow behaviour and diffusion in the mixer, and to set up design criteria needed to obtain perfect or near perfect multi-layer lamination. As a result of the study of a generic type of micro mixer and flow simulations, the need of a "separation plate" inside each mixer stage is revealed. The performance of micro machined single stage mixers has been verified by mixing experiments using the fast reaction of phenol-red and an acid. The experimental set-up takes advantage of the transparent PYREX-glass plate offering the possibility to study mixing phenomena by video microscopy.
Rat ceruloplasmin. Molecular cloning and gene expression in liver, choroid plexus, yolk sac, placenta, and testis. (1987)

A rat ceruloplasmin cDNA clone was isolated from a rat liver cDNA library and identified by partial nucleotide sequence analysis. Rat liver ceruloplasmin mRNA levels were measured during the acute phase response to inflammation by cytoplasmic dot hybridization to ceruloplasmin cDNA. Regulation of ceruloplasmin synthesis appeared to be at the mRNA level, with the concentration of ceruloplasmin mRNA increasing significantly 12 h after induction of inflammation, reaching a maximum of 350% of normal at 36 h and returning to normal levels within 60 h. Using Northern blot analysis, extrahepatic ceruloplasmin gene expression was observed in choroid plexus, yolk sac, placenta, and testis. All these tissues are at the interface between, and possibly involved in maintaining homeostasis in, adjacent extracellular compartments. No ceruloplasmin mRNA was detected in RNA from stomach and small intestine.
Hydroxamic Acids as Pharmacological Agents (2002)

A variety of hydroxamic acid derivatives have recently been touted for their potential use as inhibitors of hypertension, tumor growth, inflammation, infectious agents, asthma, arthritis, and more. Here we provide a comprehensive review of the basic medicinal chemistry and pharmacology of hydroxamic acid derivatives that have been examined as inhibitors of zinc metalloproteases, matrix metalloproteinases, leukotriene A(4) hydrolases, ureases, lipoxigenases, cyclooxygenases, as well as peptide deformilases.
Adherence and receptor relationships of Candida albicans (1991)

The cell surface of Candida albicans is composed of a variety of polysaccharides such as glucan, chitin, and mannan. The first two components primarily provide structure, while the mannan, often covalently linked to protein, constitutes the major antigen of the organism. Mannoproteins also have enzymatic activity (acid protease) and ligand-receptor functions. The complement receptors of C. albicans appear to be mannoproteins that are required for the adherence of the organism to endothelial cells. This is certainly true of the CR3-like protein of C. albicans. Proof that the CR3 is the Candida receptor for endothelial cells is derived from two observations. First, mutants lacking CR3 activity are less adherent in vitro and, in fact, less virulent. Second, the ligand recognized by the CR3 receptor (C3bi) as well as anti-CR3 antibodies blocks adherence of the organism to endothelial cells. The CR2 of C. albicans appears to promote the adherence of the organism to plastic substrates. Unlike the CR2 of mammalian cells, the Candida CR2 recognizes ligands containing the RGD sequence of amino acids in addition to the C3d ligand, which does not contain the RGD sequence. There is uncertainty as to whether the Candida CR2 and CR3 are, in fact, different proteins. A mannoprotein has also been described as the adhesin for epithelial cells. In this case, the receptor has a lectinlike activity and recognizes fucose- or glucosamine-containing glycoproteins of epithelial cells, depending on the strain of C. albicans. The oligosaccharide component of the receptor is probably not involved in ligand recognition and may serve to stabilize the receptor. However, the oligosaccharide factor 6 epitope of mannan may also provide adhesin activity in the recognition of epithelial cells. Mannoproteins can be extracted from cells by a number of reagents. Zymolyase, for instance, tends to remove structural mannoproteins, which contain relatively little protein and are linked to glucan. Reagents such as dithiothreitol, on the other hand, tend to extract mannoproteins containing higher amounts of protein that appear to have receptor function. The mannoproteins of C. albicans are dynamically expressed and may be growth phase and growth form specific.
Preliminary characterization of the procoagulant material in human ascites. (1987)

Disseminated intravascular coagulation invariably accompanies placement of peritoneovenous (LeVeen) shunts, which suggests that ascitic fluid contains procoagulant material capable of activating blood coagulation. In this study, we identified thrombogenic activity in human ascites and the hemostatic pathway by which it acts. Peritoneal fluid was removed percutaneously from patients with ascites due to various causes. Four fractions were prepared by centrifugation: cells, a low-speed, cell-free fluid, a high-speed supernatant, and the precipitate from the high-speed centrifugation. Cellular fractions from all ascitic fluids shortened a one-stage clotting time of normal pooled plasma by 68% in comparison with saline solution and endotoxin controls. Similarly, the cell-free fluids also shortened the clotting time of normal pooled plasma by 41%. The cellular and cell-free fractions shortened the clotting time of factor VIII-deficient plasma but failed to demonstrate procoagulant activity in factor VII-deficient plasma. These fractions had no effect on platelet aggregation or the platelet release reaction. The high-speed precipitate was dissociated by ethylenediaminetetra-acetate (EDTA) into fluid phase and precipitate, both of which demonstrated procoagulant activity. Furthermore, high-speed precipitate contained protein, phospholipid, and sterol in proportions similar to those of plasma membranes and contained membrane-bound vesicles as identified by means of electron microscopy. This material could be rendered inactive by heating to 100 degrees C for 2 minutes or by incubation with phospholipase C for 15 minutes. Finally, the ability of the high-speed precipitate to shorten the clotting time was prevented by preincubation with a monoclonal antibody, which is known to inhibit the procoagulant activity of human tissue factor. We suggest that several entities contribute to the procoagulant properties of human ascites, with procoagulant material deriving at least in part from peritoneal cells. The sedimentable procoagulant factor appears to be associated with cellular membranes or membrane fragments and is thromboplastin-like in its chemical composition, immunoreactivity, and substrate specificity.
The effect of parathyroid hormone on the acutely ischemic myocardium. (1990)

PTH is not beneficial in acute myocardial infarction.
Triabodies: single chain Fv fragments without a linker form trivalent trimers (1997)

A single chain Fv fragment (scFv) of the murine monoclonal antibody 11-1G10 was constructed by directly joining the C-terminal residue of the V(H) domain to the N-terminal residue of V(L). 11-1G10 is an anti-idiotype and competes with the antigen, influenza virus neuraminidase (NA), for binding to the NC41 antibody. The scFv formed stable trimers with three active antigen combining sites for NC41 Fab fragments. We propose that trimeric scFvs may be the preferred conformation for directly linked V(H)-V(L) molecules, which contrasts the formation of scFv dimers (diabodies) when the V(H) and V(L) domains are joined by short flexible linkers of between 5-10 residues. BIAcore biosensor binding experiments showed that the trimeric scFv showed an expected increase in binding affinity, due to avidity, compared to the monomeric 15-residue linked scFv. The increase in avidity of scFv trimers offers advantages for imaging and immunotherapy.
Supramolecular AD Diblock Copolymers (2005)

An error in the references cited in the published article was noticed. The correct citation for ref. 5i is provided below. The authors apologize for the oversight.
A hierarchical supra-nanostructure of HKUST-1 featuring enhanced H2 adsorption enthalpy and higher mesoporosity (2011)

A hierarchical supra-nanostructure of HKUST-1 was synthesized by directly mixing solutions of copper acetate and H3BTC (H3BTC = 1,3,5-benzenetricarboxylic acid) under ambient conditions, which exhibits enhanced H2 adsorption enthalpy and higher mesoporosity.
Antimicrobial activity of synthetic magainin peptides and several analogues. (1988)

We have previously reported the isolation of two broad-spectrum antimicrobial peptides ("magainins") from the skin of the African clawed frog Xenopus laevis. These natural peptides are active against many species of bacteria and fungi and also induce osmotic lysis of protozoa. In this report we demonstrate that synthetic magainin peptides appear to be indistinguishable from the natural products with respect to chromatographic properties and biological activity. These studies demonstrate conclusively that the magainin peptides are potent antimicrobial substances.
Attenuation of gamma interferon-induced tyrosine phosphorylation in mononuclear phagocytes infected with Leishmania donovani: selective inhibition of signaling through Janus kinases and Stat1 (1995)

The induction of gene transcription in response to gamma interferon is impaired in mononuclear phagocytes infected with Leishmania donovani, and the mechanisms involved are not fully understood. The changes in gene expression brought about by gamma interferon are thought to involve transient increases in the activities of cellular protein tyrosine kinases, including the Janus kinases Jak1 and Jak2, leading to tyrosine phosphorylation of the transcription factor Stat1. To investigate the mechanisms accounting for the impaired responses to gamma interferon, a model system for examining overall changes in protein tyrosine phosphorylation, activation of Jak1 and Jak2 and phosphorylation of Stat1 was developed in phorbol 12-myristate 13-acetate-differentiated U-937 cells. Analysis of whole-cell lysates by antiphosphotyrosine immunoblotting showed that incubation with gamma interferon brought about specific increases in phosphotyrosine labeling of several proteins. Increased labeling of these proteins occurred to similar extents in control cells and in cells that had been infected with L. donovani for 16 h. Jak1, Jak2, and Stat1 were immunoprecipitated from control and interferon-treated cells, and tyrosine phosphorylation of these proteins, detected by antiphosphotyrosine immunoblotting was used to measured their activation. Tyrosine phosphorylation of Jak1, Jak2, and Stat1 increased markedly, in a dose-dependent manner, in U-937 cells incubated with gamma interferon. In contrast, in cells infected with L. donovani, tyrosine phosphorylation of Jak1, Jak2, and Stat1 was markedly impaired. This effect was dependent upon the duration of exposure to L. donovani and was maximal and complete at 16 h. Results similar to those observed with U-937 cells were also obtained with human peripheral blood monocytes. These findings indicate that infection of human mononuclear phagocytes with L. donovani leads to impaired gamma interferon-mediated tyrosine phosphorylation and selective effects on the Jak-Stat1 pathway. Unresponsiveness to gamma interferon for activation of this pathway may explain impaired transcriptional responses in leishmania-infected cells.
Identification of MRF4: a new member of the muscle regulatory factor gene family. (1989)

We have identified a rat cDNA encoding MRF4, a new member of the muscle regulatory factor gene family that includes MyoD1, myogenin, and Myf-5. MRF4 encodes a predicted 27-kD protein that contains a conserved helix-loop-helix motif, which is a common feature of this gene family. Northern analyses indicate that MRF4 is expressed solely in skeletal muscle tissue but is not detected in most embryonic muscle cell lines. Transfection of MRF4 into C3H10T1/2 fibroblasts produces stable myogenic lineages at frequencies that are equal to or greater than those obtained when MyoD1 or myogenin are introduced into these cells. Expression of the MRF4 cDNA leads to expression of the endogenous MyoD1 and myogenin genes, although C3H10T1/2 cells expressing MyoD1 or myogenin cDNAs do not express MRF4. Interestingly, the endogenous MyoD1 and myogenin genes are negatively regulated by serum and by purified growth factors since MRF4-transfected C3H10T1/2 cells activate MyoD1 and myogenin expression only in mitogen-depleted, differentiation-induced muscle cultures. The myofiber-specific expression pattern of MyoD1 and myogenin in these cells suggests that the primary role for this muscle regulatory factor gene family may be in regulating specific terminal differentiation events that are crucial for normal skeletal muscle development.
Neutrophils Deficient in PU.1 Do Not Terminally Differentiate or Become Functionally Competent (1998)

PU.1 is an ets family transcription factor that is expressed specifically in hematopoietic lineages. Through gene disruption studies in mice we have previously shown that the expression of PU.1 is not essential for early myeloid lineage or neutrophil commitment, but is essential for monocyte/macrophage development. We have also shown that PU.1-null (deficient) neutrophils have neutrophil morphology and express neutrophil-specific markers such as Gr-1 and chloroacetate esterase both in vivo and in vitro. We now demonstrate that although PU.1-null mice develop neutrophils, these cells fail to terminally differentiate as shown by the absence of messages for neutrophil secondary granule components and the absence or deficiency of cellular responses to stimuli that normally invoke neutrophil function. Specifically, PU.1-deficient neutrophils fail to respond to selected chemokines, do not generate superoxide ions, and are ineffective at bacterial uptake and killing. The failure to produce superoxide could, in part, be explained by the absence of the gp91 subunit of nicotinamide adenine dinucleotide phosphate oxidase, as shown by our inability to detect messages for the gp91(phox) gene. Incomplete maturation of PU.1-deficient neutrophils is cell autonomous and persists in cultured PU.1-deficient cells. Our results indicate that PU.1 is not necessary for neutrophil lineage commitment but is essential for normal development, maturation, and function of neutrophils.
Demonstration of high power blue-green light emitting diode on semipolar (1122) bulk GaN substrate (2007)

Blue-green InGaN/GaN multiple-quantum-well light emitting diodes with peak emission wavelength of 480 nm were grown on low extended defect density semipolar (112̄2) bulk GaN substrates by conventional metal organic chemical vapour deposition. The calculated external quantum efficiency and output power at a drive current of 20 mA under pulsed operations (10% duty cycle) were 18% and 9 mW, respectively. The device exhibited small electroluminescence wavelength shift (4.5 nm) with drive currents ranging from 30 to 100 mA, indicating significant reduction of polarisation-related internal electric fields.
Lightweight Security for Network Coding (2008)

Under the emerging network coding paradigm, intermediate nodes in the network are allowed not only to store and forward packets but also to process and mix different data flows. We propose a low-complexity cryptographic scheme that exploits the inherent security provided by random linear network coding and offers the advantage of reduced overhead in comparison to traditional end-to-end encryption of the entire data. Confidentiality is achieved by protecting (or "locking") the source coefficients required to decode the encoded data, without preventing intermediate nodes from running their standard network coding operations. Our scheme can be easily combined with existing techniques that counter active attacks.
Pseudomonas aeruginosa tolerance to tobramycin, hydrogen peroxide and polymorphonuclear leukocytes is quorum-sensing dependent (2005)

The opportunistic human pathogen Pseudomonas aeruginosa is the predominant micro-organism of chronic lung infections in cystic fibrosis (CF) patients. P. aeruginosa colonizes the CF lungs by forming biofilm structures in the alveoli. In the biofilm mode of growth the bacteria are highly tolerant to otherwise lethal doses of antibiotics and are protected from bactericidal activity of polymorphonuclear leukocytes (PMNs). P. aeruginosa controls the expression of many of its virulence factors by means of a cell-cell communication system termed quorum sensing (QS). In the present report it is demonstrated that biofilm bacteria in which QS is blocked either by mutation or by administration of QS inhibitory drugs are sensitive to treatment with tobramycin and H2O2, and are readily phagocytosed by PMNs, in contrast to bacteria with functional QS systems. In contrast to the wild-type, QS-deficient biofilms led to an immediate respiratory-burst activation of the PMNs in vitro. In vivo QS-deficient mutants provoked a higher degree of inflammation. It is suggested that quorum signals and QS-inhibitory drugs play direct and opposite roles in this process. Consequently, the faster and highly efficient clearance of QS-deficient bacteria in vivo is probably a two-sided phenomenon: down regulation of virulence and activation of the innate immune system. These data also suggest that a combination of the action of PMNs and QS inhibitors along with conventional antibiotics would eliminate the biofilm-forming bacteria before a chronic infection is established.
Phenotypic modulation of endothelial cells by transforming growth factor-beta depends upon the composition and organization of the extracellular matrix. (1988)

Transforming growth factor beta (TGF-beta) is angiogenic in vivo. In vitro, endothelial cell proliferation is inhibited by TGF-beta. We have correlated this inhibitory effect with an increase in cellular fibronectin synthesis and deposition in a two-dimensional culture system using specific matrix coatings. The inhibitory effect was mimicked by addition of soluble fibronectin to cultures. In contrast, TGF-beta was found to elicit the formation of tube-like structures (mimicking angiogenesis) when microvascular endothelial cells were grown in three-dimensional collagen gels. In this culture system TGF-beta elicited rapid extensive formation of complex, branching, tube-like structures, while cell proliferation was not inhibited. These data confirm and support the hypothesis that TGF-beta is angiogenic and may exert some of its effects through modulation of matrix synthesis and are consistent with the hypothesis that the organization of the extracellular environment influences cellular responses to this "panregulin."
Structural models of Na+, Ca2+, and K+ channels. (1995)

The structure determination of voltage-gated channels by the combination of molecular modeling and mutagenesis experiments is a long term, iterative process. As such, the models should be considered as a work in progress, with changes expected as more data becomes available. The primary role of the models is that they assimilate the known data and provide ideas for further experiments to elucidate the real structures. Although the models presented here have already gone through two or three cycles of development and testing, many aspects remain tentative. Perhaps the most significant result so far is that the P segment was experimentally confirmed to form the ion-selective part of the channel. In a subsequent cycle of testing and modeling, the specific residues responsibility for Na+ and Ca2+ selectivity have been identified and the selectivity filter of K+ channels is now predicted to be formed by the side chains, but rather by the carbonyl oxygens of the conserved Gly-Tyr-Gly sequence backbone. As another example, the 9p residue of the P segment of K+ channels was originally modeled as either being buried in the protein or accessible channels was originally modeled as either being buried in the protein or accessible from inside the cell only. However, once mutation of this residue to histidine was found to affect blockade by extracellular TEA, protons, Zn2+ and histidine reagents (DeBiasi et al., 1993), the models were updated to have this and the hydrophilic residues in the first part of P form a helix that comprises part of the extracellular, outer vestibular of the pore. While this motif was used also for Na+ and Ca2+ pore models (see Fig. 2) where the putative helices are amphipathic, it remains to be verified. Modeling of the size and shape of the outer vestibule of K+ channels was also aided by the data for the binding of CTX in the extracellular entrance to the pore. Similarly, experiments with peptide toxins such as mu and omega conotoxins may prove useful in modeling the outer vestibules of the Na+ and/or Ca2+ channels. While important advances have been made, it is important to realize that these approaches are still very new. In the future we are likely to see improvements on both the theoretical and experimental sides which will greatly advance the process.(ABSTRACT TRUNCATED AT 400 WORDS)
Magnetic and recording characteristics of bicrystalline longitudinal recording medium formed on an MgO single crystal disk substrate (1994)

An epitaxial thin film growth has been applied to prepare bicrystalline CoCrPt longitudinal recording medium using an MgO(100) single crystal disk substrate. X-ray and TEM measurements have revealed that the magnetic layer has a bicrystalline structure which consists of two variant domains with their c-axes lying in-plane and perpendicular-to each other. The maximum medium coercivity is observed at (2n+1)/spl pi//4, while the minimum coercivity is observed at n/spl pi//2 from the MgO[010] when measured along the circumferential direction. The highest signal to noise ratio, the highest linear resolution, and the best off-track performance are observed at (2n+1)/spl pi//4 where the direction of the recording magnetic head field lies between the easy magnetization axes of the two variant domains.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>