gebhart/patrepeval huggingface dataset:
Photoresponses of transgenic Arabidopsis seedlings expressing introduced phytochrome B‐encoding cDNAs: evidence that phytochrome A and phytochrome B have distinct photoregulatory functions (1993)

The photocontrol of hypocotyl elongation has been studied in two transgenic lines of Arabidopsis thaliana which contain elevated levels of phytochrome B encoded by either an introduced rice‐ or Arabidopsis ‐derived cDNA driven by the 35S CaMV promoter. Inhibition of hypocotyl growth in etiolated seedlings of the phyB ‐transformed lines was saturated at photon fluence rates of continuous red light (R) which were markedly lower than those required for inhibition of growth in seedlings of the isogenic wild‐type (WT). Inhibition of hypocotyl growth in etiolated seedlings of the phyB ‐transgenic lines under continuous far‐red irradiation (FR), however, showed the same relationship with fluence rate as WT. Light‐grown seedlings of the phyB ‐transgenic lines responded to end‐of‐day FR by an acceleration of growth, in a manner comparable with WT. This response was unaltered when the end‐of‐day FR was extended from a 15 min pulse to 14 h of continuous irradiation. The response of light‐grown, phyB ‐transformed seedlings to decreasing R:FR ratio was also qualitatively similar to WT, i.e. increased elongation growth of the hypocotyl and petioles occurred under low R:FR quantum ratio. However, absolute elongation growth was markedly less in the transgenic seedlings at all R:FR ratios tested than in WT. Together, these data indicate that seedlings over‐expressing phytochrome B are more responsive to R than are WT, but are unaltered in their responsiveness to FR. By contrast, seedlings overexpressing phytochrome A are more responsive than WT to both R and FR; whereas the phytochrome B‐deficient mutant hy3 is unresponsive to R while retaining WT‐like responsiveness to FR. These data indicate that in WT etiolated seedlings phytochrome A mediates the effects of continuous FR, and phytochrome B the effects of continuous R. The evidence thus supports the conclusion that these two molecular species of the photoreceptor have differential regulatory roles in the plant.
Homeostasis of Human NK Cells Is Not IL-15 Dependent (2013)

IL-15 is a proinflammatory cytokine that plays an important role in the development and activation of NK cells and is a potential target for inflammatory disease therapy. Studies conducted in IL-15- and IL-15R knockout mice identified IL-15 as an important cytokine for NK cell homeostasis. Consistent with this information derived from genetically modified mice, we demonstrated that neutralizing IL-15 with a mouse anti-mouse IL-15 mAb (M96) depletes C57BL/6 mouse NK cells. An mAb directed against macaque IL-15 (Hu714MuXHu) was manufactured and demonstrated to block IL-15-induced activation of nonhuman primate (NHP) NK cells in vitro. Neutralization of macaque IL-15 by parenteral administration of Hu714MuXHu reduces (>95%) circulating NK cell counts in NHPs. A blocking mAb directed against human IL-15 (huIL-15; AMG 714) was manufactured. Unexpectedly, when human subjects were treated with the blocking anti-IL-15 Ab AMG 714 in clinical trials, no reductions in circulating NK cell counts were observed despite achieving significantly higher exposures than the levels of Hu714MuXHu needed to cause NK cell count reductions in NHPs in vivo. Both AMG 714 and Hu714MuXHu are able to block huIL-15 activity in a human T cell blast proliferation and IFN-γ production assay. Both Abs block huIL-15-mediated Stat5 activation and CD69 expression in human NK cells. Collectively, these results demonstrate that NK cell homeostasis is obligatorily dependent upon IL-15 in both mice and NHPs, but that IL-15 is dispensable for maintenance of circulating human NK cells.
Activation of Glassy Carbon Electrodes by Dispersed Metal Oxide Particles: I . Ascorbic Acid Oxidation (1984)

Various metal oxides (MOx) were dispersed onto a glassy carbon (GC) surface for the purpose of catalyzing the oxidation of ascorbic acid . Of the 37 different metal oxides examined, more than 20 showed varying degrees of rate enhancement (henceforth referred to as activation) for oxidation. The highest degree of activation was exhibited by those MOx's whose oxidation state of the metal was +3 or higher, such as zirconium oxide, ceric oxide, cobaltic oxide, chromic oxide, stannic oxide, and the previously reported alumina. The double layer capacitance was also observed to increase with MOx/GC's compared to the bare GC electrode. This increase suggested that the surface area of the GC electrodes increased due to the dispersion of MOx. The pH dependence of the activation at MOx/GC was considerably different from that at a bare GC electrode and suggested that the enhancement mechanism may involve an acceleration of a proton‐transfer step via interaction with the MOx/GC surface. A model of the physical structure of the MOx/GC surface is proposed to account for the carbon surface activation.
Role of angiotensin subtype 2 receptor in neointima formation after vascular injury. (1992)

The role of angiotensin receptor subtypes 1 and 2 was assessed on neointima formation after injury in rat carotid artery. The effects of angiotensin converting enzyme inhibition by perindopril (3 mg.kg-1 x day-1 p.o.) and selective blockade of angiotensin subtype 1 receptors by DuP 753 (5 and 30 mg.kg-1 x day-1 p.o.) were compared on proliferative response to balloon injury. In rats treated 6 days before and for 14 days after injury, perindopril significantly reduced (-76%, p < 0.01) myointimal hyperplasia. In contrast, DuP 753 at 5 mg.kg-1 x day-1 did not modify the hyperplastic response to balloon catheterization. Only at 30 mg.kg-1 x day-1 was DuP 753 able to reduce neointima formation (-47%, p < 0.05). This dose was equipotent to perindopril on the renin-angiotensin system as assessed by the pressor response to angiotensin II and angiotensin I. Therefore, blockade of subtype 1 receptors was a less effective means of suppression of myointimal growth than angiotensin converting enzyme inhibition, suggesting that another angiotensin receptor subtype or converting enzyme substrates are involved in this process. For the determination of whether angiotensin subtype 2 receptors were implicated, the specific subtype 2 receptor antagonist CGP 42112A (1 mg.kg-1 x day-1) was continuously infused perivascularly for 14 days in the vicinity of the injured carotid artery. CGP 42112A was as effective in preventing neointima formation as perindopril (-73%, p < 0.01, versus -76%, p < 0.01, respectively).(ABSTRACT TRUNCATED AT 250 WORDS)
Personality traits and Bulimia Nervosa (2016)

Bulimia Nervosa is a detrimental eating disorder that impacts millions of women. We examine the role played by socioeconomic factors and personality traits in bulimic behavior. Using data on eating disordered behavior from the National Heart, Lung, and Blood Institute Growth and Health Study, we present results showing that personality traits are significant determinants of bulimic behavior, even after controlling for race and class. This finding suggests that policies based on both the SES characteristics and the personality traits will be more effective for targeting those at risk.
Sequence similarity of a hornet (D. maculata) venom allergen phospholipase A1 with mammalian lipases (1993)

We have determined the sequence of a venom allergen phospholipase A1 from white-faced hornet (Dolichovespula maculata) by cDNA and protein sequencings. This protein of 300 amino acid residues (Dol m I) has no sequence similarity with other known phospholipases. But it has sequence similarity with mammalian lipases; about 40% identity in overlaps of 123 residues. Tests suggest that hornet phospholipase has weak lipase activity. Hornet venom has 3 major allergens, and another hornet allergen antigen 5 (Dol m V) was previously found to have sequence similarity with a mammalian testis protein and a plant leaf protein.
Automated atlas integration and interactive three-dimensional visualization tools for planning and guidance in functional neurosurgery (1998)

Many critical functionally distinct subcortical structures are not distinguishable on anatomical magnetic resonance imaging (MRI) scans. In order to provide the neurosurgeon with this missing information, a deformable volumetric atlas of the basal ganglia and thalamus has been created from the Schaltenbrand and Wahren atlas of cryogenic slices. The volumetric atlas can be automatically deformed to an individual patient's MRI. To facilitate the clinical use of the atlas, a visualization platform has been developed for preoperative and intraoperative use which permits manipulation of the merged atlas and MRI data sets in two- and three-dimensional views. The platform includes graphical tools which allow the visualization of projections of a leukotome and other surgical tools with respect to the atlas data, as well as preregistered images from any other imaging modality. In addition, a graphical interface has been designed to create custom virtual lesions using computer models of neurosurgical tools for intraoperative planning. To date this system has been employed as an adjunct to over 30 functional neurosurgical cases including surgery for movement disorders.
Onco-suppressor genes and their involvement in cancer (review). (1988)

Onco-suppressor genes are a heterogeneous set of genes that inhibit the cancer-related phenotype of cells. Because they are difficult to identify, only a few have been described. Evidence for their existence has mainly been indirect and comes from the following types of study. 1. Recessive cancer genes in higher and lower eukaryotes have been detected. If both alleles of these genes are deleted or inactivated, cancer develops. 2. Studies on cell hybrids have implicated genes which suppress various stages in the malignant conversion of normal cells e.g. immortalisation, morphological conversion and metastasis. 3. The isolation from virally induced transformants of flat, non-tumorigenic revertants in which expression of the transforming gene is not down-regulated suggests the presence of genes which suppress the effects of transformation. 4. Blocks to differentiation can be bypassed by inducing compounds or differentiation factors. 5. Studies on tumor inhibitory factors such as tumour necrosis factor and beta-TGF show that they have different effects on different types of cell-acting to promote growth in some cases and inhibit it in others. 6. The discovery of cis-acting negatice regulatory elements suggests that interaction of such elements with proteins may be important for control of gene expression particularly of infecting oncogenic viruses. 7. Suppression of the transformed phenotype of malignant cells by contact with normal cells that controls growth of neighboring cells. 8. The inhibition of proliferation of transformed cells by transfection with DNA from normal cells may be a useful method for cloning onco-suppressor genes. We discuss what is known and what is not known about this important class of gene.
Separation of Single-Walled Carbon Nanotubes with a Gel Permeation Chromatography System (2014)

A gel permeation chromatography system is used to separate aqueous sodium dodecyl sulfate suspensions of single-walled carbon nanotubes (SWCNTs). This automated procedure requires no precentrifugation, is scalable, and is found to yield monochiral SWCNT fractions of semiconducting SWCNTs with a purity of 61-95%. Unsorted and resulting monochiral fractions are characterized using optical absorption and photoluminescence spectroscopy.
Granulocyte transmigration through the endothelium is regulated by the oxidase activity of vascular adhesion protein-1 (VAP-1) (2004)

Polymorphonuclear leukocytes (PMNs) migrate from the blood into areas of inflammation by binding to the endothelial cells of blood vessels via adhesion molecules. Vascular adhesion protein-1 (VAP-1) is one of the molecules mediating leukocyte-endothelial cell interactions. It is also an endothelial cell-surface enzyme (amine oxidase) that produces reactive oxygen species during the catalytic reaction. To study the role of the enzymatic activity of VAP-1 in PMN extravasation, we used an enzymatically inactive VAP-1 mutant, specific amine oxidase inhibitors (including a novel small molecule compound), and anti-VAP-1 antibodies in several flow-dependent models. The enzyme inhibitors diminished PMN rolling on and transmigration through human endothelial cells under conditions of laminar shear stress in vitro. Notably, the enzyme inactivating point mutation abolished the capacity of VAP-1 to mediate transmigration. Moreover, the new VAP-1 inhibitor effectively prevented the extravasation of PMNs in an animal model of inflammation. These data show that the oxidase activity of VAP-1 controls PMN exit from the blood during the relatively poorly understood transmigration step.
Chemokine Class Differences in Binding to the Duffy Antigen-Erythrocyte Chemokine Receptor (1995)

The Duffy blood group antigen-erythrocyte chemokine receptor has been shown to bind to chemokines of both the C-X-C and C-C classes and to the malarial parasites Plasmodium vivax and Plasmodium knowlesi. We performed experiments to evaluate the binding properties of this receptor for the newly appreciated "C" and "non-ELR C-X-C" classes of chemokines. Binding to mouse erythrocytes was also evaluated for the first time. Whereas ELR C-X-C and C-C chemokines bound to human erythrocytes with high affinity, differences in the ability of non-ELR chemokines to act as competitive inhibitors were noted. While non-ELR chemokines were unable to displace C-X-C chemokines on human cells, they exhibited a low affinity interaction with the C-C chemokine binding site. The newly discovered C chemokine, lymphotactin, was unable to displace either C-X-C or C-C chemokines. On mouse erythrocytes, non-ELR chemokines exhibited a low affinity for both the C-X-C and C-C chemokines binding sites; again lymphotactin failed to bind. Binding competition studies using an anti-Duffy monoclonal antibody and chemokines suggested a common binding domain. These data show that the chemokine superfamily has at least four functional subdivisions, each interacting differently with the Duffy antigen-erythrocyte chemokine receptor. In addition the chemokine binding function is conserved between mouse and man. Unlike other proteins in the superfamily C and non-ELR C-X-C chemokines do not efficiently bind red blood cells, thus their role may not require clearance from circulation.
An Anti-inflammatory Function for the Complement Anaphylatoxin C5a-binding Protein, C5L2 (2005)

C5L2 is an enigmatic serpentine receptor that is co-expressed with the C5a receptor on many cells including polymorphonuclear neutrophils. The apparent absence of coupling of C5L2 with G proteins suggests that this receptor may modulate the biological activity of C5a, perhaps by acting as a decoy receptor. Alternatively, C5L2 may affect C5a function through formation of a heteromeric complex with the C5aR, or it may utilize a G protein-independent signaling pathway. Here we show that in mice bearing a targeted deletion of C5L2, the biological activity of C5a/C5a(desArg) is enhanced both in vivo and in vitro. The biological role of C5L2 thus appears to be limiting to the pro-inflammatory response to the anaphylatoxin. Accordingly, up-regulation of C5L2 may be of benefit in inflammatory states driven by C5a, including sepsis, asthma, cystic fibrosis, and chronic obstructive lung disease.
On the morphology of melt-crystallized polyethylene. III. Spherulitic organization (1981)

Abstract The lamellar microstructure of a wide range of melt-crystallized polyethylenes has been examined in the context of spherulitic organization. Radial continuity is achieved through lamellar continuity. In the simplest cases ridged or planar sheets grow outwards along b, maintain­ing their identities over distances as long as tens of micrometres, subject to changes in relative dominance depending on whether or not they can continue to grow in the most favourable direction. The generalized 'fibres’ are to be identified with dominant lamellae which lay down the framework of a spherulite’s development. Banded spherulites have S-shaped dominant sheets which are multiply-connected allowing the aver­age molecular orientation to spiral round the radius while individual lamellae are substantially untwisted. Space within spherulites is filled by branching, for which three mechanisms have been identified, namely the nucleation of new, misaligned lamellae, the incorporation of small-angle boundaries and spiral terraces associated with screw dislocations. Con­trary to prediction, the width of dominant lamellae varies much less than the Keith &amp; Padden parameter δ, but remains within a factor of 3 of 3 μm. The scale of texture revealed by the segregation of ‘impurities’ does not appear to be determined solely by the scale of the diffusion field. It is suggested that the misfit energy between adjacent non-parallel ‘fibrils’, and geometrical factors, must also be taken into account.
B Cells Regulate Murine Gammaherpesvirus 68 Latency (1999)

The dynamics of the establishment of, and reactivation from, gammaherpesviruses latency has not been quantitatively analyzed in the natural host. Gammaherpesvirus 68 (gammaHV68) is a murine gammaherpesvirus genetically related to primate gammaherpesviruses that establishes a latent infection in infected mice. We used limiting dilution reactivation (frequency of cells reactivating gammaHV68 in vitro) and limiting dilution PCR (frequency of cells carrying gammaHV68 genome) assays to compare gammaHV68 latency in normal (C57BL/6) and B-cell-deficient (MuMT) mice. After intraperitoneal (i.p.) inoculation, latent gammaHV68 was detected in the spleen, bone marrow, and peritoneal cells. Both B-cell-deficient and C57BL/6 mice established latent infection in peritoneal cells after either i.p. or intranasal (i.n.) inoculation. In contrast, establishment of splenic latency was less efficient in B-cell-deficient than in C57BL/6 mice after i.n. inoculation. Analysis of reactivation efficiency (reactivation frequency compared to frequency of cells carrying gammaHV68 genome) revealed that (i) regardless of route or mouse strain, splenic cells reactivated gammaHV68 less efficiently than peritoneal cells, (ii) the frequency of cells carrying gammaHV68 genome was generally comparable over the course of infection between C57BL/6 and B-cell-deficient mice, (iii) between 28 and 250 days after infection, cells from B-cell-deficient mice reactivated gammaHV68 10- to 100-fold more efficiently than cells from C57BL/6 mice, (iv) at 7 weeks postinfection, B-cell-deficient mice had more genome-positive peritoneal cells than C57BL/6 mice, and (v) mixing cells (ratio of 3 to 1) that reactivated inefficiently with cells that reactivated efficiently did not significantly decrease reactivation efficiency. Consistent with a failure to normally regulate chronic gammaHV68 infection, the majority of infected B-cell-deficient mice died between 100 and 200 days postinfection. We conclude that (i) B cells are not required for establishment of gammaHV68 latency, (ii) there are organ-specific differences in the efficiency of gammaHV68 reactivation, (iii) B cells play a crucial role in regulating reactivation of gammaHV68 from latency, and (iv) B cells are important for controlling chronic gammaHV68 infection.
Triple Therapy in Type 2 Diabetes (2006)

Low-dose insulin glargine combined with a sulfonylurea and metformin resulted in similar A1C improvements except for greater reductions in A1C when baseline was > or =9.5% compared with add-on maximum-dose rosiglitazone. Further, insulin glargine was associated with more hypoglycemia but less weight gain, no edema, and salutary lipid changes at a lower cost of therapy.
Multi-Agent Simulation of Self-Organizing Behaviors of Alveolar Cells In Vitro (2009)

Abstract- We present an agent-based model of cultured lung al-veolar type II (AT II) cells and simulation results that provide early insight into generative principles underpinning alveolar morphogene-sis in 3D cell cultures. We also describe a supporting framework and system-level agents that manage simulation experiments. The AT II cell-mimetic analogue comprises discrete components that represent cells and basic parts composing cell cultures. Cells are represented as quasi-autonomous agents that act based on decision logic and a set of operating principles articulated as axioms. By adhering strictly to those principles, cell agents self-organize and develop into multi-cell structures that resemble alveolar-like cysts in vitro. While it is pre-mature to assign a specific biological mapping to the in silico operat-ing principles, the findings enforce the idea that complex morphoge-netic phenomena are a consequence of adherence to a small set of epigenetic principles. We expect more advanced adaptations will provide a rigorous platform to unravel the mechanistic bases of al-veolar development and regeneration. Index Terms—Multi-agent, self-organization, autonomous systems design, agent-directed, simulation framework, behavior program-ming, systems biology 1.
HIV-1 Vaccine Development:  Constrained Peptide Immunogens Show Improved Binding to the Anti-HIV-1 gp41 MAb (2003)

The human immunodeficiency virus type I (HIV-1) transmembrane glycoprotein gp41 mediates viral entry through fusion of the target cellular and viral membranes. A segment of gp41 containing the sequence Glu-Leu-Asp-Lys-Trp-Ala has previously been identified as the epitope of the HIV-1 neutralizing human monoclonal antibody 2F5 (MAb 2F5). The 2F5 epitope is highly conserved among HIV-1 envelope glycoproteins. Antibodies directed at the 2F5 epitope have neutralizing effects on a broad range of laboratory-adapted HIV-1 variants and primary isolates. Recently, a crystal structure of the epitope bound to the Fab fragment of MAb 2F5 has shown that the 2F5 peptide adopts a beta-turn conformation [Pai, E. F., Klein, M. H., Chong, P., and Pedyczak, A. (2000) World Intellectual Property Organization Patent WO-00/61618]. We have designed cyclic peptides to adopt beta-turn conformations by the incorporation of a side-chain to side-chain lactam bridge between the i and i + 4 residues containing the Asp-Lys-Trp segment. Synthesis of extended, nonconstrained peptides encompassing the 2F5 epitope revealed that the 13 amino acid sequence, Glu-Leu-Leu-Glu-Leu-Asp-Lys-Trp-Ala-Ser-Leu-Trp-Asn, maximized MAb 2F5 binding. Constrained analogues of this sequence were explored to optimize 2F5 binding affinity. The solution conformations of the constrained peptides have been characterized by NMR spectroscopy and molecular modeling techniques. The results presented here demonstrate that both inclusion of the lactam constraint and extension of the 2F5 segment are necessary to elicit optimal antibody binding activity. The ability of these peptide immunogens to stimulate a high titer, peptide-specific immune response incapable of viral neutralization is discussed in regard to developing an HIV-1 vaccine designed to elicit a 2F5-like immune response.
T cell response to myelin basic protein epitopes in multiple sclerosis patients and healthy subjects (1991)

T cell lines and clones specific for human myelin basic protein (BP) were selected from three multiple sclerosis (MS) patients and two healthy subjects and tested for their proliferative responses to a battery of synthetic peptides, 9 to 21 amino acid residues long. The combined amino acid sequence of the peptides spanned the complete sequence of the human BP. The results suggest the development of T cells sensitized to at least four independent regions of the human BP, indicating some diversity of the human T cell repertoire to BP. However, an immunodominant T cell epitope was located in the C-terminal region, defined by residues 149-162. This epitope was recognized by T cells from three subjects out of five (one MS patient and both healthy controls) in the context of different DR specificities. Another epitope (located in the 57-75 region) which triggered one MS patient's T cell response was also recognized by a mycobacteria-specific T cell clone cross-reacting with BP.