gebhart/patrepeval huggingface dataset:
Heterotrimeric Gαq11 co‐immunoprecipitates with surface‐anchored GRP78 from plasma membranes of α2M*‐stimulated macrophages (2008)

We have previously shown that a fraction of newly expressed GRP78 is translocated to the cell surface in association with the co-chaperone MTJ-1. Proteinase and methylamine-activated alpha(2)M (alpha(2)M*) bind to cell surface-associated GRP78 activating phosphoinositide-specific phospholipase C coupled to a pertussis toxin-insensitive heterotrimeric G protein, generating IP(3)/calcium signaling. We have now studied the association of pertussis toxin-insensitive Galphaq11, with GRP78/MTJ-1 complexes in the plasma membranes of alpha(2)M*-stimulated macrophages. When GRP78 was immunoprecipitated from plasma membranes of macrophages stimulated with alpha(2)M*, Galphaq11, and MTJ-1 were co-precipitated. Likewise Galphaq11 and GRP78 co-immunoprecipitated with MTJ-1 while GRP78 and MTJ-1 co-immunoprecipitated with Galphaq11. Silencing GRP78 expression with GRP78 dsRNA or MTJ-1 with MTJ-1 dsRNA greatly reduced the levels of Galphaq11 co-precipitated with GRP78 or MTJ-1. In conclusion, we show here that plasma membrane-associated GRP78 is coupled to pertussis toxin-insensitive Galphaq11 and forms a ternary signaling complex with MTJ-1.
Synthesis of 5‐lodo‐ and 5‐nitro‐3‐indolyl phosphates as cytochemical substrates for acid phosphatase (1970)

Abstract The synthesis of 5‐iodo‐3‐indolyl and 5‐nitro‐3‐indolyl phosphate for cytochemical demonstration of acid phosphatase is reported. Enzymatic hydrolysis of these compounds liberates the corresponding indoxyl which is oxidized to the substituted indigo at an acid p H. In contrast, the 5‐bromo and the unsubstituted indoxyl are not oxidized readily at an acid p H. Comparison of the UV and visible, spectra of the disubstituted indigo has offered a partial explanation for this difference. E.S.R. measurements showed that 5,5′‐diiodoindigo, unlike 5,5′‐dibromoindigo, gives a detectable radical ion at an acid p H.
Signal Peptidase Cleavage at the Flavivirus C-prM Junction: Dependence on the Viral NS2B-3 Protease for Efficient Processing Requires Determinants in C, the Signal Peptide, and prM (1998)

Signal peptidase cleavage at the C-prM junction in the flavivirus structural polyprotein is inefficient in the absence of the cytoplasmic viral protease, which catalyzes cleavage at the COOH terminus of the C protein. The signal peptidase cleavage occurs efficiently in circumstances where the C protein is deleted or if the viral protease complex is present. In this study, we used cDNA of Murray Valley encephalitis virus (MVE) to examine features of the structural polyprotein which allow this regulation of a luminal cleavage by a cytoplasmic protease. We found that the inefficiency of signal peptidase cleavage in the absence of the viral protease is not attributable solely to features of the C protein. Inhibition of cleavage still occurred when charged residues in C were mutated to uncharged residues or when an unrelated protein sequence (that of ubiquitin) was substituted for C. Also, fusion of the C protein did not inhibit processing of an alternative adjacent signal sequence. The cleavage region of the flavivirus prM translocation signal is unusually hydrophobic, and we established that altering this characteristic by making three point mutations near the signal peptidase cleavage site in MVE prM dramatically increased the extent of cleavage without requiring removal of the C protein. In addition, we demonstrated that luminal sequences downstream from the signal peptidase cleavage site contributed to the inefficiency of cleavage.
Aliasing reduction in sub-bands of cascaded filter banks with decimation (1992)

A method for the reduction of aliasing in sub-band signals of cascaded filter banks with decimation is presented. The aliasing reduction is achieved by simple butterfly operations between filter bank outputs without influencing the reconstruction properties of analysis/synthesis systems.
Total Synthesis of a Functional Designer Eukaryotic Chromosome (2014)

Rapid advances in DNA synthesis techniques have made it possible to engineer viruses, biochemical pathways and assemble bacterial genomes. Here, we report the synthesis of a functional 272,871-base pair designer eukaryotic chromosome, synIII, which is based on the 316,617-base pair native Saccharomyces cerevisiae chromosome III. Changes to synIII include TAG/TAA stop-codon replacements, deletion of subtelomeric regions, introns, transfer RNAs, transposons, and silent mating loci as well as insertion of loxPsym sites to enable genome scrambling. SynIII is functional in S. cerevisiae. Scrambling of the chromosome in a heterozygous diploid reveals a large increase in a-mater derivatives resulting from loss of the MATα allele on synIII. The complete design and synthesis of synIII establishes S. cerevisiae as the basis for designer eukaryotic genome biology.
Simethicone in the Treatment of Infant Colic: A Randomized, Placebo-Controlled, Multicenter Trial (1994)

Although both produced perceived improvements in symptoms, simethicone is no more effective than placebo in the treatment of infantile colic.
Further evidence for ‘pain-related’ behaviours in a model of unilateral peripheral mononeuropathy (1990)

A model of experimental peripheral neuropathy producing pain-related disorders has recently been described in the rat. The present study aimed to investigate, using a different and quantifiable behavioural approach, the abnormal pain-related sensations in the animals. The neuropathy was produced by 4 ligatures tied loosely around the common sciatic nerve. 6-8 days after surgery, most of the rats exhibited pain-related disorders ipsilateral to the sciatic ligation, which became maximal 2 weeks after surgery. Mechanical noxious stimulation (pinching of the hind paw) revealed hyperalgesia in all the animals. Rats also exhibited allodynia when tested with the vocalization threshold test to paw pressure (mean vocalization thresholds were 65.5 +/- 3.6% of the preoperative control, P less than 0.01, n = 95). Tests using heat (40, 42, 44, 46 degrees C) and cold (10 degrees C) stimulation (immersion of the rat's hind paw in a bath until it was observed to struggle) indicated hyperalgesia to noxious heat (decrease of 30% in the immersion duration (ID) at a temperature of 46 degrees C), and allodynia to non-noxious heat (decrease of 30% in the temperature of the struggle threshold) and to cold stimulation (decrease by 40% in the ID). In addition, the animals showed modifications in the spontaneous postures of the affected hind paw in a natural setting, suggesting a 'spontaneous' pain-related behaviour (the mean 'pain' rating, derived from the technique used for the formalin test and numbered 0-5, was 2.8 +/- 0.4, P less than 0.01, n = 12). Lastly, sensitized responses were observed to mechanical stimulation after thermal stimulation in the non-noxious range applied to the lesioned but not the non-lesioned paw. The time course of pain-related disorders was comparable whatever the behavioural test, with recovery 2 months after surgery. These results clearly show that the neuropathy produces abnormal pain-related disorders in the rat, which are reminiscent of those observed in some human neuropathies.
In vitro evaluation of pyridine-2-azo-p-dimethylaniline cephalosporin, a new diagnostic chromogenic reagent, and comparison with nitrocefin, cephacetrile, and other beta-lactam compounds (1982)

Pyridine-2-azo-p-dimethylanaline cephalosporin (PADAC), a chromogenic reagent which is purple and changes to yellow upon cleavage of its beta-lactam ring, was evaluated in comparison with other chromogenic cephalosporins. PADAC exhibited little antimicrobial activity against gram-negative bacteria, but did have good activity (minimum inhibitory concentration, 0.12 to 0.5 microgram/ml) against Staphylococcus aureus, a quality comparable to nitrocefin. Nitrocefin, however, demonstrated an unexpected and uniquely potent activity against Streptococcus faecalis (minimum inhibitory concentration, less than or equal to 0.06 to 0.12 microgram/ml) The relative hydrolysis rate of PADAC when subjected to six different beta-lactamases was substantially greater than that of cephacetrile, but less than that of nitrocefin. The relative hydrolysis rates of PADAC and nitrocefin were comparable with type IIIa beta lactamase and the derived from Bacillus cereus. The inhibition of beta-lactamase hydrolysis of the chromogenic cephalosporin substrates by six enzyme-stable inhibitors was generally greater with PADAC than with nitrocefin. Unlike nitrocefin, PADAC mixed with 50% human serum or various broth culture media showed no evidence of color change or degradation over several hours. The subsequent enzyme hydrolysis rates of such mixtures were the same as in phosphate buffer. Beta-lactamase-containing bacterial suspensions and clinical specimens containing such bacteria produced positive visual and spectrophotometric color changes when mixed with PADAC or nitrocefin. Although color changes occurred more slowly with PADAC than with nitrocefin, PADAC was not adversely influenced (non-enzyme-related color change) by the protein content of specimens. PADAC appears to be a promising alternative for beta-lactamase diagnostic testing in the clinical and research microbiology laboratory.
Giant tunneling magnetoresistance in Co2MnSi∕Al–O∕Co2MnSi magnetic tunnel junctions (2006)

Magnetic tunnel junctions (MTJs) with a stacking structure of Co2MnSi∕Al–O∕Co2MnSi were fabricated using magnetron sputtering system. Fabricated MTJ exhibited an extremely large tunneling magnetoresistance (TMR) ratio of 570% at low temperature, which is the highest TMR ratio reported to date for an amorphous Al–O tunneling barrier. The observed dependence of tunneling conductance on bias voltage clearly reveals the half-metallic energy gap of Co2MnSi. The origins of large temperature dependence of TMR ratio were discussed on the basis of the present results.
Endometrial Cells Derived From Donor Stem Cells in Bone Marrow Transplant Recipients (2004)

These findings demonstrate that endometrial cells can originate from donor-derived bone marrow cells and suggest that nonuterine stem cells contribute to the regeneration of endometrial tissue.
Exosome-associated Tau Is Secreted in Tauopathy Models and Is Selectively Phosphorylated in Cerebrospinal Fluid in Early Alzheimer Disease (2011)

Background: Tau is secreted unconventionally, possibly explaining increased CSF phosphotau levels in early AD. Results: M1C cells secrete selectively phosphorylated, exosomal tau. These characteristics in early AD CSF tau suggest that CSF tau is secreted, not shed from dead neurons. Conclusion: Tau secretion occurs early and may explain lesion spreading in AD. Significance: Secretion biomarkers may become revolutionary prospective AD diagnostics.
Some General Properties of Nonlinear Elements. II. Small Signal Theory (1958)

The simplest types of nonlinear capacitor modulators, demodulators, and negative conductance amplifiers, in which components at only two signal frequencies are present, are studied by means of the well-known small-signal analysis. The results of this analysis of course agree with the general energy relations of Part I, but in addition give the gain, bandwidth, terminal admittances, and sensitivity (to changes in the terminal admittances or in the local oscillator drive) of these devices, and show the way in which these quantities depend on the amount of nonlinearity. In general, the bandwidth of all of these devices approaches zero as the nonlinearity approaches zero. Three cases are considered; f1 is the local oscillator frequency. 1) Noninverting modulator and demodulator-signal frequencies fl and f+=f1+fl. This device is stable and yields maximum gain with matched source and load. Under matched conditions the gain is equal to the ratio of output to input frequency; for widely separated signal frequencies the modulator has substantial gain, the demodulator an equal loss. Only a relatively small amount of nonlinearity is required to attain a bandwidth equal to the low-signal frequency. Since source and load are matched the sensitivity is zero. 2) Inverting modulator and demodulator-signal frequencies fl and f-=f1-fl. This device is potentially unstable; its input conductance is negative and match is impossible.
A Contraceptive Peptide Vaccine Targeting Sulfated Glycoprotein ZP2 of the Mouse Zona Pellucida1 (1999)

In this study, we have mapped and characterized a B cell epitope of sulfated glycoprotein ZP2 (ZP2) as a step toward the development of a multi-epitope zona pellucida (ZP) vaccine. Recombinant polypeptides expressed by random deoxyribonuclease-digested fragments of ZP2 cDNA were screened for binding to IE-3, a monoclonal antibody to murine ZP2. Positive clones contained cDNA inserts encoding polypeptide corresponding to ZP2(103-134). When normal or ovariectomized female mice were immunized with three overlapping peptides that span this region of ZP2 (101-120, 111-130, 121-140), only ZP2(121-140) elicited IgG antibodies that reacted with mouse ovarian ZP, indicative of the presence of native B epitope and helper T cell epitope in ZP2(121-140). To more finely map the ZP2 B cell epitope, a random peptide display library was screened with the IE-3 antibody, and a consensus tetramer sequence VxYK that matched the ZP2(123-126) sequence VRYK was located. Competitive immunofluorescence analysis with single alanine-substituted VxYK peptides ranked the relative contribution of the three critical B cell epitope residues as Y > V > K. A chimeric peptide was constructed that contained the YRYK motif of ZP2 and a bovine RNase T cell epitope. Although (C57BL/6xA/J) F1 (B6AF1) female mice immunized with the chimeric peptide developed ZP antibody response, this peptide elicited antibody only in mice of the histocompatibility complex (MHC) H-2(k or b) haplotype. In contrast, ZP2(121-140) peptide elicited antibody in inbred mice with three additional mouse MHC haplotypes. Moreover, although ZP2(121-140) contained a T cell epitope, no oophoritis was observed after immunization of B6AF1 mice with ZP2(121-140) in complete Freund's adjuvant (CFA). In a preliminary trial, female B6AF1 mice immunized with ZP2(121-140) in CFA had reduced litter sizes as compared with mice injected with CFA alone.
Syntheses of Heterocyclic Compounds Involving Aromatic Lithiation Reactions in the Key Step (1983)

Heteroatom-directed aromatic lithiation reactions for the syntheses of several heterocyclic ring systems and naturally occurring compounds which have not been synthesised or which have been synthesised only through considerably longer routes by the usual methods are reviewed in this article. 1. Introduction 2. Aromatic Lithiation Reactions 3. Synthesis of Basic Heterocyclic Ring Systems 4. Utility of the New Synthetic Methods 5. Strategies to Improve Yields in Aromatic Lithiation Reactions
Turbo equalization with low complexity decoder (2002)

Turbo equalization (TE) is an iterative receiver algorithm repeating equalization and channel decoding to improve receiver performance. As equalization and decoding are performed several times, the complexity of the TE receiver increases respectively. Furthermore, the decoder needs to provide probability information as output, which increases the computational burden even more. In this paper we introduce a new method to reduce the decoding complexity of the TE receiver. This soft trellis decoding (STD) technique utilises information obtained from the previous decoding step to select those trellis metrics that need to be recalculated. Hence, the most unlikely trellis branches are eliminated. We evaluate STD performance in the Enhanced General Packet Radio System (EGPRS) platform by simulations. We show that STD reaches performance close to full trellis decoding, but requires only a fraction of the computational power.
Dynamic fluid connectivity during steady-state multiphase flow in a sandstone (2017)

The current conceptual picture of steady-state multiphase Darcy flow in porous media is that the fluid phases organize into separate flow pathways with stable interfaces. Here we demonstrate a previously unobserved type of steady-state flow behavior, which we term "dynamic connectivity," using fast pore-scale X-ray imaging. We image the flow of N<sub>2</sub> and brine through a permeable sandstone at subsurface reservoir conditions, and low capillary numbers, and at constant fluid saturation. At any instant, the network of pores filled with the nonwetting phase is not necessarily connected. Flow occurs along pathways that periodically reconnect, like cars controlled by traffic lights. This behavior is consistent with an energy balance, where some of the energy of the injected fluids is sporadically converted to create new interfaces.
Clonal analysis of autoantibody-producing cell precursors in the preimmune B cell repertoire. (1988)

Evidence for anti-self-reactivity in the preimmune B cell repertoire has been well documented. The present study aimed to determine the frequency of antibody-forming cell precursors in this repertoire whose Ig V regions impart reactivity to "self" or autologous Ag. Clones were activated in vitro with LPS and their secreted IgM antibody was assayed for reactivity by direct binding to cell surface or intracellular Ag. An IL-4-containing lymphokine mixture was added to the clonal cultures to induce the secretion of IgG1. The reactivity of secreted IgG1 with Ag would more closely resemble the binding required to activate B cells through their monomeric surface IgM and/or IgD. The results indicate a high frequency of precursors secreting IgM with reactivity to intracellular Ag, namely 1 in 37 +/- 6 B cells, with a marked paucity of response to cell surface molecules. The repertoire was markedly deficient in precursors secreting IgG1 able to bind to intracellular Ag, with only one clone detected by the screening of 3.0 x 10(6) spleen cells. No positives were detected for cell surface Ag. This suggested that the frequency of clones in the preimmune repertoire that express IgR with sufficient affinity to bind "self" molecules must be very low.
EXTRACELLULAR PROTEINS IN FUNGI: A CYTOLOGICAL AND MOLECULAR PERSPECTIVE (1999)

Protein secretion is a vital process in fungi. For many, the secretion of hydrolytic enzymes provides a crucial step in their nutrition in nature. However, in recent years the list of different types of secreted proteins that have been discovered has extended significantly. These have been shown to have a diversity of functions including toxic molecule transport and control of desiccation. The majority of secreted proteins are glycosylated and our understanding of this aspect of fungal biochemistry has also extended in recent years. This review addresses the process of protein secretion from the cytological, biochemical and genetical standpoints. Advances in technology in many areas of scientific approach have enabled a better and understanding of this important process in fungi.
B‐lymphocyte quiescence, tolerance and activation as viewed by global gene expression profiling on microarrays (2000)

Self-tolerance is achieved by deleting or regulating self-reactive lymphocytes at a series of cellular checkpoints placed at many points along the developmental pathways to plasma cells and effector T cells. At each checkpoint, what are the molecular pathways that determine whether a lymphocyte remains quiescent, begins dividing, differentiates or dies? In splenic B cells, the decision between quiescence, tolerance by anergy, and activation provides a tractable setting to explore these issues by global gene expression profiling on DNA microarrays. Here we discuss the application of microarrays to illuminate a set of cell fate decisions that appear to be determined by summation of numerous small changes in expression of stimulatory and inhibitory genes. Many genes with known or predicted inhibitory functions are highly expressed in naive, quiescent B cells, notably the signal inhibitor SLAP and DNA-binding proteins of the Kruppel family (LKLF, BKLF, GKLF), Tsc-22, GILZ, Id-3, and GADD45. Activation of naive B cells, triggered by acute binding of antigen to the B-cell receptor, involves a rapid decrease in expression of these inhibitory genes. Promitotic genes are induced in parallel, including c myc, LSIRF/IRF4, cyclin D2, Egr-1 and Egr-2, as are the anti-apoptotic gene A1 and genes for the T-cell-attracting chemokines MIP-1alpha and beta. B-cell tolerance through the process of anergy, induced by chronic binding of self antigen, maintains expression of the inhibitory genes found in quiescent B cells and induces an additional set of inhibitory genes. The latter include inhibitors of signaling - CD72, neurogranin, pcp4 - and additional inhibitors of gene expression such as SATB1, MEF2C, TGIF and Nab-2. The effects of tolerance, the immunosuppressive drug FK506 and other modulators of calcium or MAPK signaling allow individual gene responses to be linked to different signal transduction pathways. The global molecular profiles obtained illustrate how quiescence and anergy are actively maintained in circulating B cells, how these states are switched to clonal expansion and how they could be better emulated by pro-tolerogenic drugs.
The metabolism of native and malondialdehyde-altered low density lipoproteins by human monocyte-macrophages (1981)

We have recently shown that cultured human monocyte-macrophages degraded 125I-labeled low density lipoprotein (125I-nativeee-LDL) by a saturable high-affinity process with maximal velocity at 25-30 microgram protein/ml (Fogelman et al., 1980, Proc. Nat. Acad. Sci. USA. 77:2214-2218). We now describe studies of the binding of 125I-native-LDL at 4 degrees C and the effects of chloroquine, Ca2+ concentration, and reductive methylation on high-affinity 125I-native-LDL degradation that indicate that native-LDL is processed by the monocyte-macrophages via the classic LDL receptor pathway. The high-affinity degradation of 125I-native-LDL increased substantially when monocyte-macrophages were exposed to the lipoprotein deficient-fraction of serum (LPDS) for periods as brief as 4 hours, and was 25-fold greater than that of lymphocytes. Freshly isolated monocytes that had never been exposed to LPDS also demonstrated high-affinity degradation of 125I-nativ-LDL. When these monocytes were cultured for 7 days in a medium containing native-LDL at a concentration (186 microgram protein/ml) greatly in excess of that apparently needed to saturate the high-affinity process, there was more than a 10-fold increase in 125I-native-LDL high-affinity degradation. LDL modified by treatment with malondialdehyde was processed by a second high-affinity cell surface receptor that appears identical to the "scavenger" receptor that processes acetylated LDL (Goldstein, et al., 1979, Proc. Nat. Acad. Sci. USA. 76: 333-337).
One more role for the gut: microbiota and blood brain barrier. (2016)

The gut microbiota is composed of trillions of microbes that perform several tasks which are essential to our physiology. Recent emerging evidences have suggested the important contribution of gut microbiota in several biological functions of mamals, such as the regulation of the immune system, metabolism, intestinal development or brain physiology (1-4). In fact, recent work, mainly performed in experimental model of Multiple Sclerosis (MS), have demonstrated that resident commensal microbiota can modulate central nervous system (CNS) autoimmunity (5-8). The microbiota is now known to shift the balance between protective and pathogenic immune responses, in the CNS, but also in other organs. A growing body of evidence in animal support also the concept that the gut microbiota influences emotional behavior (9,10) and that its products and metabolites may promote metabolic effects such as reduced body weight, reduced adiposity, and improved glucose control (11). As regards, CNS physiology, the gut microbiota influence synaptogenesis, regulate neurotransmitters and neurotrophic factors release and function (4).