gebhart/patrepeval huggingface dataset:
Endodermal Nodal-related signals and mesoderm induction in Xenopus (2000)

In Xenopus, mesoderm induction by endoderm at the blastula stage is well documented, but the molecular nature of the endogenous inductive signals remains unknown. The carboxy-terminal fragment of Cerberus, designated Cer-S, provides a specific secreted antagonist of mesoderm-inducing Xenopus Nodal-Related (Xnr) factors. Cer-S does not inhibit signalling by other mesoderm inducers such as Activin, Derrière, Vg1 and BMP4, nor by the neural inducer Xnr3. In the present study we show that Cer-S blocks the induction of both dorsal and ventral mesoderm in animal-vegetal Nieuwkoop-type recombinants. During blastula stages Xnr1, Xnr2 and Xnr4 are expressed in a dorsal to ventral gradient in endodermal cells. Dose-response experiments using cer-S mRNA injections support the existence of an endogenous activity gradient of Xnrs. Xnr expression at blastula can be activated by the vegetal determinants VegT and Vg1 acting in synergy with dorsal (beta)-catenin. The data support a modified model for mesoderm induction in Xenopus, in which mesoderm induction is mediated by a gradient of multiple Nodal-related signals released by endoderm at the blastula stage.
Type 1 T-helper cell predominance and interleukin-12 expression in the gut of patients with Crohn's disease. (1997)

Crohn's disease (CD) is a chronic bowel inflammatory disorder in which the pathogenic role of immune alterations has been suggested, but the immunologic mechanisms responsible for the inflammatory reaction are still poorly understood. We investigated the profile of cytokine secretion by T-cell clones generated from gut tissue specimens of four patients with active CD, five patients with ulcerative colitis, and four patients with noninflammatory gut disorders (NIGDs). The great majority of CD4+ T-cell clones generated from the gut of patients with CD produced high levels of interferon-gamma (IFN-gamma) but low or undetectable amounts of interleukin-4 (IL-4), whereas substantial proportions of CD4+ T-cell clones derived from the gut of patients with either ulcerative colitis or NIGDs produced IL-4 in addition to IFN-gamma. The immunohistochemical analysis revealed high numbers of activated CD4+ T cells showing IFN-gamma but not IL-4 reactivity, as well as substantial proportions of IL-12-containing macrophages, in the intestinal lamina propria and muscularis propria of patients with CD, whereas these cells were very rare or undetectable in patients with NIGDs. Culturing T cells from gut biopsy specimens of a patient with CD in the presence of a neutralizing anti-IL-12 antibody down-regulated the development of IFN-gamma-producing CD4+ T cells. These findings suggest that a critical event in the initiation of bowel inflammatory lesions in CD may involve up-regulation of IL-12 production, resulting in conditions that maximally promote type 1 T-helper immune responses.
A survey on wireless mesh networks (2005)

Wireless mesh networks (WMNs) have emerged as a key technology for next-generation wireless networking. Because of their advantages over other wireless networks, WMNs are undergoing rapid progress and inspiring numerous applications. However, many technical issues still exist in this field. In order to provide a better understanding of the research challenges of WMNs, this article presents a detailed investigation of current state-of-the-art protocols and algorithms for WMNs. Open research issues in all protocol layers are also discussed, with an objective to spark new research interests in this field.
Xylocandin: A new complex of antifungal peptides. II. Structural studies and chemical modifications. (1987)

Xylocandins A1, A2, B1, B2, C1, C2, D1 and D2 are new antifungal peptides isolated from Pseudomonas cepacia ATCC 39277. The molecular weights of the xylocandins were determined by fast atom bombardment mass spectrometry (A1 m/z 1,215; A2 1,199; B1 1,229; B2 1,213; C1 1,097; C2 1,081; D1 1,083; D2 1,067). Each xylocandin is a cyclic peptide containing glycine, serine, asparagine (1-3 residues), beta-hydroxytyrosine, and an unusual amino acid with the formula C18H37NO5. Additionally A1, A2, D1 and D2 contain 2,4-diaminobutyric acid; A1, B1, C1 and D1 contain erythro-beta-hydroxyasparagine; and A1, A2, B1 and B2 contain xylose. For each xylocandin pair, an erythro-beta-hydroxyasparagine residue in the first component of the pair is thus replaced by an asparagine in the second component, accounting for the 16 dalton mass difference for each pair. Chemical modification of A1 and A2 at the diaminobutyric acid and beta-hydroxytyrosine residues was used to probe structural requirements for activity.
Morphogens in motion: Growth control of the neural tube (2005)

The entire vertebrate nervous system develops from a simple epithelial sheet, the neural plate which, along development, acquires the large number and wide variety of neuronal cell types required for the construction of a functional mature nervous system. These include processes of growth and pattern formation of the neural tube that are achieved through complicated and tightly regulated genetic interactions. Pattern formation, particularly in the vertebrate central nervous system, is one of the best examples of a morphogen-type of function. Cell cycle progression, however, is generally accepted to be dependent on cell-intrinsic factors. Recent studies have demonstrated that proliferation of neural precursors is also somehow controlled by secreted signaling molecules, well-known by their role as morphogens, such as fibroblast growth factor (FGF), vertebrate orthologs of the Drosophila wingless (Wnt), hedgehog (Hh), and transforming growth factor beta (TGF-beta) families, that in turn regulate the activity of factors controlling cell cycle progression. In this review we will summarize the experimental data that support the idea that classical morphogens can be reused to regulate proliferation of neural precursors.
The cytochrome P450 3A4 inducer metyrapone is an activator of the human pregnane X receptor (1999)

Conference Article| August 01 1999 The cytochrome P450 3A4 inducer metyrapone is an activator of the human pregnane X receptor M. C. Wright M. C. Wright 1University Medicine, Level D, Southampton General Hospital, Tremona Road, Southampton SO 16 6YD, U.K. Search for other works by this author on: This Site PubMed Google Scholar Author and article information Publisher: Portland Press Ltd Received: March 03 1999 Online ISSN: 1470-8752 Print ISSN: 0300-5127 © 1999 Biochemical Society1999 Biochem Soc Trans (1999) 27 (4): 387–391. https://doi.org/10.1042/bst0270387 Article history Received: March 03 1999 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Cite Icon Cite Get Permissions Citation M. C. Wright; The cytochrome P450 3A4 inducer metyrapone is an activator of the human pregnane X receptor. Biochem Soc Trans 1 August 1999; 27 (4): 387–391. doi: https://doi.org/10.1042/bst0270387 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search Keywords: CAT, chloramphenicol acetyltransferase, CYP, cytochrome P450, ER6, everted repeat sequence, GR, glucocorticoid receptor, LAGS, low-affinity glucocorticoid-binding site, PXR, pregnane X receptor, SXR, steroid and xenobiotic receptor, TAT, tyrosine aminotransferase This content is only available as a PDF. © 1999 Biochemical Society1999 Article PDF first page preview Close Modal You do not currently have access to this content.
Solid state [Trends/developments] (1996)

As linewidths and other lithographic features of ICs shrink, and the number of transistors on a chip mushrooms, functions galore are being combined on a single die. The ultimate result of this trend will be the system-on-a-chip, in which all circuitry-for a computer, a cellular phone, a microelectromechanical actuator, or a solid-state camera-will be housed within a couple of square centimeters of silicon. The Semiconductor Industry Association, San Jose, California, predicts that the trend toward greater complexity will endure throughout this decade and the next. Nonetheless, to keep the technology moving onward, the association's National Technology Roadmap for Semiconductors, finalized late in 1994, identified many key advances as prerequisites to progress. These are: power management, optical techniques for IC production, interconnect technology, and environmental factors. Some of the development highlights discussed are powerful multimedia engines, graphics united with main memory, and DRAM with on-board microprocessors.
Structural and functional analogy between pneumolysin and proaerolysin (1997)

Pneumolysin and proaerolysin are bacterial toxins that form pores in host cells by oligomerization. We propose that they may have similar structures despite a poor sequence identity. The crystal structure of proaerolysin reveals a protein composed of four domains, arranged in the shape of an elongated comma. Electron microscopy of the pneumolysin monomer shows a similar arrangement of domains. The sequence of pneumolysin recognizes the template of proaerolysin from a library of protein folds. A three-dimensional model of pneumolysin has been constructed by the comparative approach using the structure of proaerolysin. This model, together with results on the activity of site-specific mutants and the positions of antigenic sites, has been used to propose functional roles of individual domains.
High‐Resolution Scanning Transmission Electron Microscopy (HRSTEM) Techniques: High‐Resolution Imaging and Spectroscopy Side by Side (2012)

This work presents an overview of high-resolution scanning transmission electron microscopy (HRSTEM) techniques and exemplifies the novel quantitative characterization possibilities that have emerged from recent advances in these methods. The synergistic combination of atomic resolution imaging and spectroscopy provided by HRSTEM is highlighted as a unique feature that can provide a comprehensive analytical description of material properties at the nanoscale. State-of-the-art high-angle annular dark field and annular bright field examples are depicted as well as the use of X-ray energy-dispersive spectroscopy and electron energy-loss spectroscopy for probing samples properties at the atomic scale. In addition, promising techniques such as cathodoluminescence, confocal HRSTEM, and diffraction mapping are introduced. The presented examples and results indicate that HRSTEM-related techniques are fundamental tools for comprehensive assessment of properties at the atomic scale.
Peptides corresponding to the CD8 and CD4 binding domains of HLA molecules block T lymphocyte immune responses in vitro. (1994)

CD4 and CD8 are cell surface glycoproteins that serve as co-receptors for Ag with the TCR. Recent studies have shown that both CD4 and CD8 interact with conserved regions of MHC class II and class I, respectively. To investigate further the roles of CD4 and CD8 in the immune response, we prepared synthetic peptides corresponding to the HLA sequences with which CD4 and CD8 are thought to interact. The peptide corresponding to residues 222 to 235 of the HLA class I heavy chain blocked the differentiation of human CTL precursors into active effect cells but affected neither the ability of PBLs to proliferate in response to mitogen nor the cytotoxic activity of established CTLs. In contrast, the peptide corresponding to residues 134 to 152 of the HLA-DR beta-chain inhibited the differentiation of CTL precursors, the proliferative response of freshly isolated PBL, and the proliferation of an established alloreactive CD4+ T cell clone to Ag. The inhibitory effect of the DR.134-152 peptide on CTL differentiation could be overcome by addition of exogenous IL-2 to the limiting dilution cultures, whereas the effect of the HLA-1.222-235 peptide was unaffected by exogenous IL-2. These results directly demonstrate a functional role for these regions of MHC molecules and underscore the central role of both CD4 and CD8 in the effective initiation of a CTL response.
Effects of Evolocumab (AMG 145), a Monoclonal Antibody to PCSK9, in Hypercholesterolemic, Statin-Treated Japanese Patients at High Cardiovascular Risk (2014)

In Japanese patients at high cardiovascular risk with hypercholesterolemia on stable statin therapy, evolocumab significantly reduced LDL-C and was well tolerated during this 12-week study.
Design, synthesis and topoisomerase II inhibition activity of 4'-demethylepipodophyllotoxin-lexitropsin conjugates. (1996)

The design and synthesis of 4'-demethylepipodophyllotoxin-lexitropsin conjugates capable of inhibiting the actions of topoisomerase II are described. Siteselective topoisomerase II cleavage was observed in the presence of the new inhibitors, as determined by DNA sequencing. Additional topoisomerase II cleavage sites were observed with the new compounds that seem to be characteristic of the minor groove-binding lexitropsin moieties. Compound 17, having three pyrrole units in its binding moiety, exhibited distinct topoisomerase-mediated sites of cleavage at positions 4258, 4257, 4255 and 4247 of the pBR322 DNA fragment. These results demonstrate that conjugation with minor groove-binding moieties can alter or increase the number of topoisomerase II-induced cleavable sites and contribute to our understanding of the cytostatic activity of these compounds against KB cancer cell lines.
DNA Strands from Denatured Duplexes are Translocated through Engineered Protein Nanopores at Alkaline pH (2009)

Nanopores are under development for the detection of a variety of analytes and the investigation of chemical reactions at the single molecule level. In particular, the analysis of nucleic acid molecules is under intense investigation, including the development of systems for rapid, low-cost DNA sequencing. Here, we show that DNA can be translocated through an engineered alphaHL protein pore at pH 11.7, a value at which dsDNA is denatured. Therefore, the alphaHL pore is sufficiently stable to entertain the possibility of direct nanopore sequencing of genomic dsDNA samples, which are more readily obtained and handled than ssDNA.
CVII.—Synthesis from glucose of an octamethylated disaccharide. Methylation of sucrose and maltose (1905)

T. Purdie and J. C. Irvine, J. Chem. Soc., Trans., 1905, 87, 1022 DOI: 10.1039/CT9058701022
A new strategy to decrease N -methyl- d -aspartate (NMDA) receptor coactivation: Inhibition of d -serine synthesis by converting serine racemase into an eliminase (2001)

Serine racemase is a brain-enriched enzyme that synthesizes d-serine, an endogenous modulator of the glycine site of N-methyl-d-aspartate (NMDA) receptors. We now report that serine racemase catalyzes an elimination reaction toward a nonphysiological substrate that provides a powerful tool to study its neurobiological role and will be useful to develop selective enzyme inhibitors. Serine racemase catalyzes robust elimination of l-serine O-sulfate that is 500 times faster than the physiological racemization reaction, generating sulfate, ammonia, and pyruvate. This reaction provides the most simple and sensitive assay to detect the enzyme activity so far. We establish stable cell lines expressing serine racemase and show that serine racemase can also be converted into a powerful eliminase in cultured cells, while the racemization of l-serine is inhibited. Likewise, l-serine O-sulfate inhibits the synthesis of d-serine in primary astrocyte cultures. We conclude that the synthetic compound l-serine O-sulfate is a better substrate than l-serine as well as an inhibitor of d-serine synthesis. Inhibition of serine racemase provides a new strategy to selectively decrease NMDA receptor coactivation and may be useful in conditions in which overstimulation of NMDA receptors plays a pathological role.
Human CD8+CXCR3+ T cells have the same function as murine CD8+CD122+ Treg (2009)

The importance of CD8(+)CD122(+) Treg in the maintenance of immune homeostasis has been previously demonstrated in mice. Because the expression pattern of CD8 and CD122 in humans is different from that in mice, human CD8(+) Treg that correspond to the murine CD8(+)CD122(+) Treg have not been identified. In this study, we performed DNA microarray analyses to compare the gene expression profiles of CD8(+)CD122(+) cells and CD8(+)CD122(-) cells in mice and found that CXCR3 was preferentially expressed in CD8(+)CD122(+) cells. When we analyzed the expression of CD122 and CXCR3 in murine CD8(+) cells, we observed a definite population of CD122(+)CXCR3(+) cells. CD8(+)CXCR3(+) cells in mice showed similar regulatory activities to CD8(+)CD122(+) cells by in vivo and in vitro assays. While CD8(+)CD122(+)CXCR3(+) cells are present in mice, CD8(+)CXCR3(+) cells, but not CD8(+)CD122(+) cells, are present in humans. In the in vitro assay, human CD8(+)CXCR3(+) cells showed the regulatory activity of producing IL-10 and suppressing IFN-gamma production from CD8(+)CXCR3(-) cells. These results suggest that human CD8(+)CXCR3(+) T cells are the counterparts of murine CD8(+)CD122(+) Treg.
Somatic mutations in MYD88 and CXCR4 are determinants of clinical presentation and overall survival in Waldenström macroglobulinemia (2014)

Whole genome sequencing has revealed activating somatic mutations in MYD88 (L265P) and CXCR4 in Waldenström macroglobulinemia (WM). CXCR4 somatic mutations in WM are the first ever reported in human cancer and are similar to nonsense (NS) and frameshift (FS) germline mutations found in warts, hypogammaglobulinemia, infections and myelokathexis (WHIM) syndrome. We genotyped lymphoplasmacytic cells from 175 WM patients and observed significantly higher bone marrow (BM) disease involvement, serum immunoglobulin-M levels, and symptomatic disease requiring therapy, including hyperviscosity syndrome in those patients with MYD88(L265P)CXCR4(WHIM/NS) mutations (P < .03). Patients with MYD88(L265P)CXCR4(WHIM/FS) or MYD88(L265P)CXCR4(WILDTYPE (WT)) had intermediate BM and serum immunoglobulin-M levels; those with MYD88(WT)CXCR4(WT) showed lowest BM disease burden. Fewer patients with MYD88(L265P) and CXCR4(WHIM/FS or NS) vs MYD88(L265P)CXCR4(WT) presented with adenopathy (P < .01), further delineating differences in disease tropism based on CXCR4 status. Neither MYD88 nor CXCR4 mutations correlated with SDF-1a (RS1801157) polymorphisms in 54 patients who were genotyped for these variants. Unexpectedly, risk of death was not impacted by CXCR4 mutation status, but by MYD88(WT) status (hazard ratio 10.54; 95% confidence interval 2.4-46.2, P = .0018). Somatic mutations in MYD88 and CXCR4 are important determinants of clinical presentation and impact overall survival in WM. Targeted therapies directed against MYD88 and/or CXCR4 signaling may provide a personalized treatment approach to WM.
Low‐Density Lipoprotein Reduction and Magnitude of Cardiovascular Risk Reduction (2009)

The authors examined the relationship between the magnitude of low-density lipoprotein cholesterol (LDL-C) reduction and the magnitude of cardiovascular risk reduction. From the Veterans Integrated Service Network 1 databases, the authors selected 54,611 patients with prevalent ischemic heart disease, peripheral vascular disease or diabetes mellitus, and >or=2 documented LDL-C levels who were followed between 1997 and 2006. The outcome was defined as acute myocardial infarction or revascularization. Preoutcome LDL-C reduction was categorized as follows: <10 mg/dL, reference; >or=10 but <40 mg/dL, small reduction; >or=40 but <70 mg/dL, moderate reduction; >or=70 mg/dL, large reduction. Proportional hazards were used to determine the hazard ratio for the outcome for each LDL-C reduction category compared with the reference. Results revealed a graded relationship between the magnitude of reduction in LDL-C and cardiovascular risk reduction. Stratified analyses demonstrated these findings to be robust regardless of initial LDL-C levels or whether patients achieved "target" final LDL-C values of <100 mg/dL.
Six unrelated HLA-DR-matched adults recognize identical CD4+ T cell epitopes from influenza A haemagglutinin that are not simply peptides with high HLA-DR binding affinities. (1998)

Influenza A/Beijing/32/92 (H3N2) haemagglutinin (HA)-specific short-term CD4+ T cell lines were generated from six unrelated HLA-DR0701, 1501 positive adults (aged 27-60 years) 3 months following administration of an influenza subunit vaccine containing HA A/Beijing/32/92. Epitope recognition was examined using 118 HA A/Beijing/32/92-specific 16mer peptides which overlapped by 11 residues and which spanned the entire molecule. Following influenza vaccination the donors recognized identical HA peptides. The selected peptides represented HA regions which have been free from extensive drift mutation since the emergence of human H3N2 influenza A strains. Using DAP DR7.0701 cells (a murine cell line expressing HLA-DR0701) as antigen-presenting cells the majority of CD4+ T cell responses were shown to be HLA-DR0701 restricted. The relationship between HA peptide recognition and relative strength of HA peptide-HLA-DR0701 binding was then explored in a competition assay with biotinylated CLIP peptide. Although peptides representing dominant HA epitopes bound to DR0701, the relationship between relative strength of binding and immunodominance was complex, and many strongly binding peptides, particularly those with glycosylation sites and showing inter-strain variation, were not recognized. These results illustrate the control HLA class II exerts over CD4+ T cell HA epitope selection in unrelated adult humans. Immunodominance appears not to be directly related to the relative strength of HA peptide-HLA class II binding, and thus reflects complex interactions between antigen processing, intracellular competition for HLA binding, TCR repertoires and repeated exposure to different strains of influenza A viruses.
Calibration of Cameras with Radially Symmetric Distortion (2008)

We present algorithms for plane-based calibration of general radially distorted cameras. By this, we understand cameras that have a distortion center and an optical axis such that the projection rays of pixels lying on a circle centered on the distortion center form a right viewing cone centered on the optical axis. The camera is said to have a single viewpoint (SVP) if all such viewing cones have the same apex (the optical center); otherwise, we speak of NSVP cases. This model encompasses the classical radial distortion model [5], fisheyes, and most central or noncentral catadioptric cameras. Calibration consists in the estimation of the distortion center, the opening angles of all viewing cones, and their optical centers. We present two approaches of computing a full calibration from dense correspondences of a single or multiple planes with known euclidean structure. The first one is based on a geometric constraint linking viewing cones and their intersections with the calibration plane (conic sections). The second approach is a homography-based method. Experiments using simulated and a broad variety of real cameras show great stability. Furthermore, we provide a comparison with Hartley-Kang's algorithm [12], which, however, cannot handle such a broad variety of camera configurations, showing similar performance.
Gaussian beams from variable groove depth grating couplers in planar waveguides (1993)

Analysis, fabrication, and characterization of variable groove depth planar waveguide grating couplers are presented. A formula is derived to describe the grating groove depth variation necessary to produce an outcoupled beam of arbitrary profile. A variable depth grating for producing a Gaussian beam profile is fabricated on a waveguide by ion-beam etching through a scanning slit apparatus. A photoresist grating placed on the waveguide provides a mask to define the grating etched onto the waveguide. The near-field irradiance of the outcoupled beam is measured and shown to approach a Gaussian profile.