gebhart/patrepeval huggingface dataset:
Convenient Preparation of 1,3-Bis(dimethylamino)trimethinium Perchlorate, Tetrafluoroborate and Hexafluorophosphate (1996)

Formylation of ethyl vinyl ether with (chloromethylene)dimethylammonium chloride prepared from dimethylformamide and oxalyl chloride or phosgene followed by successive treatment with dimethylamine and 70% perchloric acid leads to 1,3-bis(dimethylamino)trimethinium perchlorate 1a in high yield. Similarly, work-up of the reaction mixture after formylation with hexafluorophosphoric acid or dimethylamine tetrafluoroborate afforded 1,3-bis(dimethylamino)trimethinium hexafluorophosphate 1b or tetrafluoroborate 1c , respectively.
Implication of nonspecific cellular infiltrates in renal transplant patients with chronic allograft nephropathy (2013)

Objective To investigate the implication of nonspecific cellular infiltrates in biopsy of chronic allograft nephropathy and the prognosis.Methods Recipients indicated to renal biopsyproven CAN were analyzed from June 2007 to June 2009 retrospectively,and classified into three groups according to the Banff 2009 criteria:chronic active T-cell-mediated rejection (CTMR),chronic active antibody-mediated rejection (CAMR),interstitial fibrosis and tubular atrophy not otherwise specified (NOS).All the cases were followed up for 2 years.CD4,CD8,CD20 and CD3 expression,and C4d deposits were investigated.Results Eighty-three cases were enrolled in the study,diagnosed as having CTMR in 34 cases (40.9％),CAMR in 12 cases (14.6％),and NOS in 37 cases (44.5％).There was significant difference in total interstitial inflammation (ti),peritubular capillaritis (ptc) and C4d deposition among CTMR,CAMR and NOS groups.The number of CD4+ and CD8+ in CTMR group was increased as compared with CAMR and NOS groups.The 2-yeard renal graft survival in CTMR,NOS and CAMR groups was 73.5％,78.4％ and 41.7％ respectively.The prognosis in CAMR group was worst.Conclusion CAMR predicated a worse graft survival.Infiltration of CD4+ and CD8 + cells may help to make the diagnosis of CTMR.

Key words: 
Graft rejection; T-lymphocytes; Antibodies; Kidney transplantation; Pathology
Energy Spectroscopy of Andreev Levels between Two Superconductors (1997)

We perform energy spectroscopy of Andreev reflection processes occurring at two superconducting electrodes connected in series via a ballistic two dimensional channel, by measuring the voltage dependence of that part of the conductance modulated by the macroscopic phase difference. The amplitude of the modulation oscillates as a function of energy and the phase exhibits an abrupt shift close to $\ensuremath{\pi}$ at the energy for which the amplitude is minimum. A microscopic theoretical description ascribes the phenomenon to the precursor of a bound state formed between the two superconductors.
Univariate Density Estimation by Orthogonal Series (1978)

Journal Article Univariate density estimation by orthogonal series Get access H. D. BRUNK H. D. BRUNK Department of Statistics, Oregon State UniversityCorvallis Search for other works by this author on: Oxford Academic Google Scholar Biometrika, Volume 65, Issue 3, December 1978, Pages 521–528, https://doi.org/10.1093/biomet/65.3.521 Published: 01 December 1978 Article history Received: 01 July 1977 Revision received: 01 January 1978 Published: 01 December 1978
Synthesis and intramolecular hydrogen bonding and biochemical studies of clitocine, a naturally occurring exocyclic amino nucleoside (1988)

The total synthesis of clitocine [6-amino-5-nitro-4-(beta-D-ribofuranosylamino)pyrimidine] (1), a nucleoside recently isolated from the mushroom Clitocybe inversa, has been accomplished. Glycosylation of 4,6-diamino-5-nitropyrimidine (4) with 1-O-acetyl-2,3,5-tri-O-benzoyl-D-ribofuranose afforded the protected nucleoside 6-amino-5-nitro-4-[(2,3,5-tri-O-benzoyl-beta-D-ribofuranosyl) amino]pyrimidine (5) in good yield exclusively as the beta-anomer. Deprotection of 5 with NaOMe/MeOH gave 1 as an 11.5:1 mixture of the beta- and alpha-anomers, respectively. Recrystallization from MeOH, followed by chromatography, afforded 1 containing less than 1% of its alpha-anomer. X-ray crystal data revealed a planar aglycon moiety in clitocine with each oxygen atom of the nitro group intramolecularly hydrogen bonded to the hydrogen atoms of the two adjacent amino functions. Clitocine inhibited L1210 cells in vitro with an ID50 of 3 X 10(-8) M. Clitocine was also found to be a substrate and inhibitor of adenosine kinase with a Ki value of 3 X 10(-6) M.
Proinflammatory Cytokines Regulate Expression of the Lymphatic Endothelial Mitogen Vascular Endothelial Growth Factor-C (1998)

Vascular endothelial growth factor (VEGF) is a prime regulator of normal and pathological angiogenesis. Three related endothelial cell growth factors, VEGF-B, VEGF-C, and VEGF-D were recently cloned. We have here studied the regulation of VEGF-C, a lymphatic endothelial growth factor, by angiogenic proinflammatory cytokines. Interleukin (IL)-1beta induced a concentration- and a time-dependent increase in VEGF-C, but not in VEGF-B, mRNA steady-state levels in human lung fibroblasts. The increase in VEGF-C mRNA levels was mainly due to increased transcription rather than elevated mRNA stability as detected by the nuclear run-on method and by following mRNA decay in the presence of an inhibitor of transcription, respectively. In contrast, angiopoietin-1 mRNA, encoding the ligand for the endothelial-specific Tek/Tie-2 receptor, was down-regulated by IL-1beta. Tumor necrosis factor-alpha and IL-1alpha also elevated VEGF-C mRNA steady-state levels, whereas the IL-1 receptor antagonist and dexamethasone inhibited the effect of IL-1beta. Experiments with cycloheximide indicated that the effect of IL-1beta was independent of protein synthesis. Hypoxia, which is an important inducer of VEGF expression, had no effect on VEGF-B or VEGF-C mRNA levels. IL-1beta and tumor necrosis factor-alpha also stimulated the production of VEGF-C protein by the fibroblasts. Cytokines and growth factors have previously been shown to down-regulate VEGF receptors in vascular endothelial cells. We found that the mRNA for the VEGF- and VEGF-C-binding VEGFR-2 (KDR/Flk-1) was stimulated by IL-1beta in human umbilical vein endothelial cells, whereas the mRNA levels of VEGFR-1 (Flt-1) and VEGFR-3 (Flt-4) were not altered. Our data suggest that in addition to VEGF, VEGF-C may also serve as an endothelial stimulus at sites of cytokine activation. In particular, these results raise the possibility that certain proinflammatory cytokines regulate the lymphatic vessels indirectly via VEGF-C.
Serum Lipids in Hypercholesterolemic Men and Women Consuming Oat Bran and Amaranth Products (2000)

ABSTRACT One hundred‐eighty hypercholesterolemic subjects following the National Cholesterol Education Program Step One Diet were randomly divided into six groups (30 ± 2/group). Group 1 served as the control and received no fiber supplements. The fiber supplemented groups received 50 g/day of oat bran or amaranth from various sources: Group 2 (oat bran muffins); Group 3 (amaranth muffins); Group 4 (Oat Bran O's); Group 5 (Oat Bran Flakes); and Group 6 (a variety of oat bran products). Fasting serum total cholesterol (FSTC), low density‐, very low density‐, and high density‐lipoprotein cholesterol (LDL‐C, VLDL‐C, and HDL‐C) and serum triacylglycerols were measured before and after the 28‐day intervention. Three‐day diet records were completed before and after intervention. Subjects reduced ( P &lt; 0.05) the mean intake of total and saturated fat, and cholesterol. FSTC dropped more than twice as much ( P &lt; 0.05) as was observed with fat modification alone (Group 1 = ‐0.31 mmol/L), when oat bran was provided as flakes (Group 5 = ‐0.86 mmol/L) or in a variety of forms (Group 6 = ‐0.75 mmol/L). If the initial ratio of HDL‐C to FSTC was low, then supplementation did not decrease FSTC to the extent observed when the initial ratio was high. Compliance with the dietary interventions was best when the subjects gave the product a rating of ≤2.0 (on a 1–4 hedonic scale, with 1 being excellent). We can conclude from these data that fiber supplementation to reduce serum cholesterol is most effective in hypercholesterolemic individuals that have a greater proportion of HDL‐C. In addition, not all the oat bran products evaluated were able to lower cholesterol to the same extent, indicating that the ability of soluble fiber to reduce FSTC can be compromised by other dietary factors such as insoluble fiber.
An Engineered Microbial Platform for Direct Biofuel Production from Brown Macroalgae (2012)

Prospecting macroalgae (seaweeds) as feedstocks for bioconversion into biofuels and commodity chemical compounds is limited primarily by the availability of tractable microorganisms that can metabolize alginate polysaccharides. Here, we present the discovery of a 36-kilo-base pair DNA fragment from Vibrio splendidus encoding enzymes for alginate transport and metabolism. The genomic integration of this ensemble, together with an engineered system for extracellular alginate depolymerization, generated a microbial platform that can simultaneously degrade, uptake, and metabolize alginate. When further engineered for ethanol synthesis, this platform enables bioethanol production directly from macroalgae via a consolidated process, achieving a titer of 4.7% volume/volume and a yield of 0.281 weight ethanol/weight dry macroalgae (equivalent to ~80% of the maximum theoretical yield from the sugar composition in macroalgae).
A human placental cDNA clone that encodes nonhistone chromosomal protein HMG-1 (1989)

From a human placental lambda gt11 cDNA library, we have isolated a cDNA clone that encodes the entire 215-residue amino acid sequence of HMG-1. Analysis of an internal sequence similarity suggests that the DNA-binding domains of HMG-1 are separated by a rather long and flexible linker segment. Southern blotting of DNA digested with BamHI indicated a highly variable number of genes (or pseudogenes) for HMG-1 in different species. Characterization of HMG-1 mRNA expression by Northern blotting showed that three mRNA species of approximately 1.0, 1.4 and 2.4 kb were expressed in all mammalian organs and cell lines examined. These included several rat organs at different stages of development. Northern analysis also suggested the occurrence of HMG-1 mRNA in an invertebrate and a plant species.
Nerve fibre discharges, cerebral potentials and sensations induced by CO2 laser stimulation. (1984)

Short radiant heat pulses, emitted by a high power CO2 laser, were used to investigate single nociceptor activity, cerebral potentials and concomitant sensations. Stimuli of 20 and 50 ms duration with different intensities were randomly applied to the hairy skin of the hand. Microelectroneurography was performed from the radial nerve at the wrist; 26 stable recordings were evaluated. Pre- and post-stimulus EEG segments were recorded from vertex versus linked ear lobes. Sensation was assessed on an eight-step category scale, an adjective scale, and by reaction times. In some experiments an A-fibre block was applied in order to isolate C-fibre responses. The main results were: Short heat stimuli activate C-units. In addition one of two identified A delta-units responded. None of the 15 A beta-units investigated was activated by the heat pulses. Short heat stimuli evoked cerebral potentials having a main vertex positive component at about 400 ms. These potentials were ascribed to A delta-fibre input. Laser induced pain consisted of an immediate stinging component, followed by a burning pain which often lasted several seconds. Reaction time to first pain ranged from 400-500 ms. Weak laser stimuli induced non-painful sensations mostly of tactile character. High correlations were found between the number of spikes elicited by a given stimulus and the intensity of the evoked sensation. Intensity discrimination, as evaluated by measures of Signal Detection Theory, was better in the peripheral C-units than in the subjective ratings. If conduction of A-fibres was blocked by pressure, A delta-related cerebral potential components vanished.(ABSTRACT TRUNCATED AT 250 WORDS)
Human T Cells That Are Able to Produce IL-17 Express the Chemokine Receptor CCR6 (2008)

Some pathways of T cell differentiation are associated with characteristic patterns of chemokine receptor expression. A new lineage of effector/memory CD4+ T cells has been identified whose signature products are IL-17 cytokines and whose differentiation requires the nuclear receptor, RORgammat. These Th17 cells are critical effectors in mouse models of autoimmune disease. We have analyzed the association between chemokine receptor expression and IL-17 production for human T cells. Activating cord blood (naive) CD4+ T cells under conditions driving Th17 differentiation led to preferential induction of CCR6, CCR9, and CXCR6. Despite these data, we found no strong correlation between the production of IL-17 and expression of CCR9 or CXCR6. By contrast, our analyses revealed that virtually all IL-17-producing CD4+ T cells, either made in our in vitro cultures or found in peripheral blood, expressed CCR6, a receptor found on approximately 50% of CD4+ memory PBL. Compared with CD4+CD45RO+CCR6- cells, CD4+CD45RO+CCR6+ cells contained at least 100-fold more IL-17A mRNA and secreted 100-fold more IL-17 protein. The CCR6+ cells showed a similar enrichment in mRNA for RORgammat. CCR6 was likewise expressed on all IL-17-producing CD8+ PBL. CCR6 has been associated with the trafficking of T, B, and dendritic cells to epithelial sites, but has not been linked to a specific T cell phenotype. Our data reveal a fundamental feature of IL-17-producing human T cells and a novel role for CCR6, suggesting both new directions for investigating IL-17-related immune responses and possible targets for preventing inflammatory injury.
The X window system, version 11 (1990)

The X Window System® has become widely accepted by many manufacturers. X provides network transparent access to display servers, allowing local and remote client programs to access a user's display. X is used on high performance workstation displays as well as terminals, and client programs run on everything from micro to super computers. This paper describes the trade-offs and basic design decisions made during the design of X Version 11. We presume familiarity with the paper describing X Version 10.
Worldwide Overview of the Current Status of Lung Cancer Diagnosis and Treatment (2012)

Lung cancer is the leading worldwide cause of cancer deaths. Smoking is the dominant cause of lung cancer and smoking cessation is the established method to reduce lung cancer mortality. While lung cancer risk is reduced in former smokers, they have a lifelong increase in risk, compared to never-smokers. Novel chemoprevention strategies, such as oral or inhaled prostacyclin analogs, hold promise for these subjects. Low-dose spiral computed tomography screening reduced lung cancer mortality by 20% in high-risk heavy smokers older than 50 years. However, the high false-positive rate (96%) means that screened patients required controlled follow-up in experienced centers. An increasing percentage of patients with advanced lung cancer have molecular drivers in genes for which oral tyrosine kinase inhibitors have been developed.
Bone Marrow Stromal Cells Generate Muscle Cells and Repair Muscle Degeneration (2005)

Bone marrow stromal cells (MSCs) have great potential as therapeutic agents. We report a method for inducing skeletal muscle lineage cells from human and rat general adherent MSCs with an efficiency of 89%. Induced cells differentiated into muscle fibers upon transplantation into degenerated muscles of rats and mdx-nude mice. The induced population contained Pax7-positive cells that contributed to subsequent regeneration of muscle upon repetitive damage without additional transplantation of cells. These MSCs represent a more ready supply of myogenic cells than do the rare myogenic stem cells normally found in muscle and bone marrow.
Probabilistic Non-linear Principal Component Analysis with Gaussian Process Latent Variable Models (2005)

Summarising a high dimensional data set with a low dimensional embedding is a standard approach for exploring its structure. In this paper we provide an overview of some existing techniques for discovering such embeddings. We then introduce a novel probabilistic interpretation of principal component analysis (PCA) that we term dual probabilistic PCA (DPPCA). The DPPCA model has the additional advantage that the linear mappings from the embedded space can easily be nonlinearised through Gaussian processes. We refer to this model as a Gaussian process latent variable model (GP-LVM). Through analysis of the GP-LVM objective function, we relate the model to popular spectral techniques such as kernel PCA and multidimensional scaling. We then review a practical algorithm for GP-LVMs in the context of large data sets and develop it to also handle discrete valued data and missing attributes. We demonstrate the model on a range of real-world and artificially generated data sets.
A Limulus intracellular coagulation inhibitor with characteristics of the serpin superfamily. Purification, characterization, and cDNA cloning. (1994)

A Limulus intracellular coagulation inhibitor, designated LICI, was isolated from hemocytes of the Japanese horseshoe crab (Tachypleus tridentatus), using three steps of chromatography, including dextran sulfate-Sepharose CL-6B, Sephacryl S-200, and Mono S. LICI is a single-chain glycoprotein with an apparent M(r) = 48,000 estimated by SDS-polyacrylamide gel electrophoresis. It blocks the amidolytic activities of Limulus lipopolysaccharide-sensitive serine protease, factor C, by forming a covalent 1:1 complex with the protease. The second-order rate constant for inhibition of factor C was 2.5 x 10(6) M-1 s-1 at 37 degrees C. LICI also inhibited human alpha-thrombin, rat salivary kallikrein, bovine plasmin, and trypsin but not Limulus clotting enzyme, Limulus factor B, bovine factor Xa, human factor XIa, human tissue plasminogen activator, human urokinase, chymotrypsin, elastase, and papain. Glycosaminoglycans such as heparin and heparan sulfate had no effect on the inhibitory activity. A cDNA coding for LICI was isolated from a hemocyte cDNA library. The open reading frame of the 1,257-base pair cDNA codes for the mature protein of 394 amino acids, of which 223 residues were confirmed by amino acid sequence analysis. LICI shows significant sequence identities to members of the serpin superfamily, such as human plasminogen activator inhibitor type 2 (40%) and human monocyte/neutrophil elastase inhibitor (39%). LICI contains a putative reactive site, -Arg-Ser-, at the corresponding position present in several inhibitors of the serpin superfamily. The subcellular localization, determined using an anti-LICI polyclonal antibody, indicated that LICI colocates with the Limulus serine protease zymogens in large granules in the hemocyte.
Omega amino acids in peptide design: incorporation into helices. (1996)

Incorporation of easily available achiral omega-amino acid residues into an oligopeptide results in substitution of amide bonds by polymethylene units of an aliphatic chain, thereby providing a convenient strategy for constructing a peptidomimetic. The central Gly-Gly segment of the helical octapeptide Boc-Leu-Aib-Val-Gly-Gly-Leu-Aib-Val-OMe(1) has been replaced by delta-amino-valeric acid (delta-Ava) residue in the newly designed peptide Boc-Leu-Aib-Val-delta-Ava-Leu-Aib-Val-OMe(2). 1H-nmr results clearly suggest that in the apolar solvent CDCl3, the delta-Ava residue is accommodated into a folded helical conformation, stabilized by successive hydrogen bonds involving the NH groups of Val(3), delta-Ava(4), and Leu(5). The delta-Ava residue must adopt a gauche-gauche-trans-gauche-gauche conformation along the central polymethylene unit of the aliphatic segment, a feature seen in an energy-minimized model conformation based on nmr parameters. The absence of hydrogen bonding functionalities, however, limits the elongation of the helix. In fact, in CDCl3, the folded conformation consists of an N-terminal helix spanning residues 1-4, followed by a Type II beta-turn at residues 5 and 6, whereas in strongly solvating media like (CD3)2SO, the unfolding of the N-terminal helix results in beta-turn conformations at Leu(1)-Aib(2). The Type II beta-turn at the Leu(5)-Aib(6) segment remains intact even in (CD3)2SO.CD comparisons of peptides 1 and 2 reveal a "nonhelical" spectrum for 2 in 2,2,2-trifluoroethanol.
Stimulation of MAP kinase by v‐raf transformation of fibroblasts fails to induce hyperphosphorylation of transfected tau (1995)

A proportion of the microtubule-associated protein, tau, is in an elevated state of phosphorylation in foetal and adult brain whereas all of the tau in paired helical filaments, which are characteristic of Alzheimer's disease is hyperphosphorylated; it is important therefore to elucidate the mechanisms that regulate tau phosphorylation. Here we describe results that show that although MAP kinase can hyperphosphorylate tau in vitro, activation of MAP kinase in transformed fibroblasts does not result in hyperphosphorylation of transfected tau, whereas glycogen synthase kinase-3 beta (GSK-3 beta) when co-transfected with tau does result in tau hyperphosphorylation. The findings imply that GSK-3 beta may be a stronger candidate than MAP kinase for inducing tau hyperphosphorylation in vivo.
Antigens derived from melanocyte differentiation proteins: self‐tolerance, autoimmunity, and use for cancer immunotherapy (2002)

A large set of peptide antigens presented by class I major histocompatibility complex (MHC) molecules on human and murine melanomas and recognized by CD8+ T cells have been defined. These peptides represent attractive candidates for the development of therapeutic and/or prophylactic approaches to treat this cancer. However, the majority of the peptides that are presented by multiple tumors and recognized by T cells from multiple patients arise from proteins that are also expressed in normal melanocytes. It is expected that immune responses to such peptides will be compromised by self-tolerance or, alternatively, that stimulation of effective immune responses will be accompanied by autoimmune vitiligo. In this review, we describe a preclinical model to evaluate these issues and recent data to suggest that tolerance can be overcome to generate effective antitumor responses. This model also allows the rapid and systematic examination of parameters for the effective use of synthetic peptide vaccines.
Size-dependent DNA mobility in nanochannels (2007)

Nanofluidic slits are used to investigate surface interactions during electrophoresis between DNA molecules and channel walls. The channels have vertical dimensions of 19 and 70nm and contain no sieving matrix. Size-dependent mobility is observed for DNA in the 19nm channels. We present a model for double stranded DNA mobility in the nanochannels that accurately predicts the size dependence of the DNA mobility in the range of 2000–10000bp. Due to surface interactions, the DNA mobility in the nanochannels scales as N−1∕2. These results suggest that the notion of free solution DNA electrophoresis breaks down due to surface interactions in nanoscale environments.
ChemInform Abstract: POTENTIAL ANTINEOPLASTICS. PART 1. ARYLAMINOTETRAHYDRO‐2H‐1,3,2‐OXAZAPHOSPHORINE 2‐OXIDES, ANALOGS OF CYCLOPHOSPHAMIDE (1977)

Abstract Durch Umsetzung von 3‐Amino‐ l‐propanol (I) mit den aromatischen Aminen (II) in Gegenwart von POCl 3 und Tri‐ äthylamin in Methylenchlorid werden in 4 ‐ 51%iger Ausbeute die lostgruppenfreien Cyclophosphamidderivate (III) erhalten.