gebhart/patrepeval huggingface dataset:
Constitutive mutants of the protein kinase STE11 activate the yeast pheromone response pathway in the absence of the G protein. (1992)

STE4 encodes the beta-subunit of a heterotrimeric guanine nucleotide-binding protein (G protein) that is an early and essential component of the pheromone signal transduction pathway. From a ste4 deletion strain we have isolated both dominant and recessive suppressors that show increased transcription of pheromone responsive genes and have regained the ability to mate, albeit at a low level. Each of these suppressor mutations suppresses ste4 and ste5 deletions but not deletions in STE7, STE11, or STE12. Among the dominant mutations, we have identified two alleles of STE11, a gene that encodes a protein kinase activity essential for mating. One allele contains an alteration in the putative regulatory domain of the protein kinase; the second allele has an alteration in the catalytic site. In strains carrying these mutations, a second protein kinase required for mating, STE7, becomes hyperphosphorylated, just as it does in wild-type cells treated with pheromone. Thus, a protein kinase cascade appears to be an essential feature of the response pathway and probably connects the receptor/G protein to an identified transcription factor, STE12.
A macromolecular complex of β 2 adrenergic receptor, CFTR, and ezrin/radixin/moesin-binding phosphoprotein 50 is regulated by PKA (2002)

It has been demonstrated previously that both the cystic fibrosis transmembrane conductance regulator (CFTR) and beta(2) adrenergic receptor (beta(2)AR) can bind ezrinradixinmoesin-binding phosphoprotein 50 (EBP50, also referred to as NHERF) through their PDZ motifs. Here, we show that beta(2) is the major adrenergic receptor isoform expressed in airway epithelia and that it colocalizes with CFTR at the apical membrane. beta(2)AR stimulation increases CFTR activity, in airway epithelial cells, that is glybenclamide sensitive. Deletion of the PDZ motif from CFTR uncouples the channel from the receptor both physically and functionally. This uncoupling is specific to the beta(2)AR receptor and does not affect CFTR coupling to other receptors (e.g., adenosine receptor pathway). Biochemical studies demonstrate the existence of a macromolecular complex involving CFTR-EBP50-beta(2)AR through PDZ-based interactions. Assembly of the complex is regulated by PKA-dependent phosphorylation. Deleting the regulatory domain of CFTR abolishes PKA regulation of complex assembly. This report summarizes a macromolecular signaling complex involving CFTR, the implications of which may be relevant to CFTR-dysfunction diseases.
Summarizing multiple aspects of model performance in a single diagram (2001)

A diagram has been devised that can provide a concise statistical summary of how well patterns match each other in terms of their correlation, their root‐mean‐square difference, and the ratio of their variances. Although the form of this diagram is general, it is especially useful in evaluating complex models, such as those used to study geophysical phenomena. Examples are given showing that the diagram can be used to summarize the relative merits of a collection of different models or to track changes in performance of a model as it is modified. Methods are suggested for indicating on these diagrams the statistical significance of apparent differences and the degree to which observational uncertainty and unforced internal variability limit the expected agreement between model‐simulated and observed behaviors. The geometric relationship between the statistics plotted on the diagram also provides some guidance for devising skill scores that appropriately weight among the various measures of pattern correspondence.
Does Spirituality Represent the Sixth Factor of Personality? Spiritual Transcendence and the Five‐Factor Model (1999)

This study reports on the development of the Spiritual Transcendence Scale, a measure designed to capture aspects of the individual that are independent of the qualities contained in the Five‐Factor Model of Personality (FFM). Using two separate samples of undergraduate students including both self‐report ( N s = 379 and 356) and observer data ( N = 279), it was shown that Spiritual Transcendence: (a) was independent of measures of the FFM; (b) evidenced good cross‐observer convergence; and (c) predicted a wide range of psychologically salient outcomes, even after controlling for the predictive effects of personality. Given the long theoretical pedigree of Transcendence in the psychological literature, it was argued that Spiritual Transcendence represents a broad‐based motivational domain of comparable breadth to those constructs contained in the FFM and ought to be considered a potential sixth major dimension of personality.
The Nucleoprotein Is Required for Efficient Coronavirus Genome Replication (2004)

The construction of a set of transmissible gastroenteritis coronavirus (TGEV)-derived replicons as bacterial artificial chromosomes is reported. These replicons were generated by sequential deletion of nonessential genes for virus replication, using a modified TGEV full-length cDNA clone containing unique restriction sites between each pair of consecutive genes. Efficient activity of TGEV replicons was associated with the presence of the nucleoprotein provided either in cis or in trans. TGEV replicons were functional in several cell lines, including the human cell line 293T, in which no or very low cytopathic effect was observed, and expressed high amounts of heterologous protein.
Intratumoral modulation of the inducible co-stimulator ICOS by recombinant oncolytic virus promotes systemic anti-tumour immunity (2017)

Emerging data suggest that locoregional cancer therapeutic approaches with oncolytic viruses can lead to systemic anti-tumour immunity, although the appropriate targets for intratumoral immunomodulation using this strategy are not known. Here we find that intratumoral therapy with Newcastle disease virus (NDV), in addition to the activation of innate immunity, upregulates the expression of T-cell co-stimulatory receptors, with the inducible co-stimulator (ICOS) being most notable. To explore ICOS as a direct target in the tumour, we engineered a recombinant NDV-expressing ICOS ligand (NDV-ICOSL). In the bilateral flank tumour models, intratumoral administration of NDV-ICOSL results in enhanced infiltration with activated T cells in both virus-injected and distant tumours, and leads to effective rejection of both tumours when used in combination with systemic CTLA-4 blockade. These findings highlight that intratumoral immunomodulation with an oncolytic virus expressing a rationally selected ligand can be an effective strategy to drive systemic efficacy of immune checkpoint blockade.
Induction of apoptosis by monoclonal antibody anti-APO-1 class switch variants is dependent on cross-linking of APO-1 cell surface antigens (1992)

Apoptosis, programmed cell death, was previously shown to be induced by the mAb anti-APO-1 (IgG3, kappa) by binding to the APO-1 cell surface Ag, a new member of the nerve growth factor/TNF receptor superfamily. To investigate the role of the Ig H chain Fc regions we compared induction of apoptosis by the original mAb IgG3 anti-APO-1 with anti-APO-1 F(ab')2 fragments and different anti-APO-1 isotypes (IgG1, IgG2b, IgG2a, and IgA) isolated by sequential sublining. We found that IgG3 was the most active isotype; IgG1, IgG2a, and IgA showed intermediate activity, and IgG2b and F(ab')2 were inactive. Cytotoxic activity of the inactive or less active antibody preparations was fully reconstituted by protein A, anti-mouse Ig, or anti-mouse Ig F(ab')2, respectively. Thus, APO-1-mediated induction of apoptosis was dependent on efficient cross-linking of APO-1 cell surface Ag, indirectly augmented by anti-APO-1 Fc-Fc self-aggregation. Because of their different in vitro activity we selected IgG3-, IgG2b-, and IgA anti-APO-1 to test their antitumor activity against solid human B lymphoblastoid tumors in SCID mice. The isotypes showed a different serum half-life (IgG3: 9.2-10.4 days, IgG2b: 1.9-2.6 days, and IgA: 14.1-29.2 h) and a different initial tumor localization 4 h after i.p. injection (IgG3 around the blood vessels, IgG2b homogeneously, and IgA heterogeneously distributed in the tumor). All antibody preparations induced tumor regression by induction of apoptosis, even IgG2b anti-APO-1 inactive in vitro without cross-linking. The activity of IgA anti-APO-1, which did not mediate complement-dependent cytotoxicity or antibody-dependent cellular cytotoxicity indicates that apoptosis may be used as the main if not the only mechanism of induction of tumor regression in vivo. As with in vitro, IgG3 anti-APO-1 was the most effective isotype also in vivo. This result suggests that cross-linking of APO-1 on the tumor cell surface may also be required for tumor regression by apoptosis in vivo. Taken together, our data show that selective targeting of apoptosis to tumors may be an efficient antitumor mechanism.
recA-like genes from three archaean species with putative protein products similar to Rad51 and Dmc1 proteins of the yeast Saccharomyces cerevisiae (1996)

The process of homologous recombination has been documented in bacterial and eucaryotic organisms. The Escherichia coli RecA and Saccharomyces cerevisiae Rad51 proteins are the archetypal members of two related families of proteins that play a central role in this process. Using the PCR process primed by degenerate oligonucleotides designed to encode regions of the proteins showing the greatest degree of identity, we examined DNA from three organisms of a third phylogenetically divergent group, Archaea, for sequences encoding proteins similar to RecA and Rad51. The archaeans examined were a hyperthermophilic acidophile, Sulfolobus sofataricus (Sso); a halophile, Haloferax volcanii (Hvo); and a hyperthermophilic piezophilic methanogen, Methanococcus jannaschii (Mja). The PCR generated DNA was used to clone a larger genomic DNA fragment containing an open reading frame (orf), that we refer to as the radA gene, for each of the three archaeans. As shown by amino acid sequence alignments, percent amino acid identities and phylogenetic analysis, the putative proteins encoded by all three are related to each other and to both the RecA and Rad51 families of proteins. The putative RadA proteins are more similar to the Rad51 family (approximately 40% identity at the amino acid level) than to the RecA family (approximately 20%). Conserved sequence motifs, putative tertiary structures and phylogenetic analysis implied by the alignment are discussed. The 5' ends of mRNA transcripts to the Sso radA were mapped. The levels of radA mRNA do not increase after treatment with UV irradiation as do recA and RAD51 transcripts in E.coli and S.cerevisiae. Hence it is likely that radA in this organism is a constitutively expressed gene and we discuss possible implications of the lack of UV-inducibility.
Noradrenergic pain modulation (2006)

Norepinephrine is involved in intrinsic control of pain. Main sources of norepinephrine are sympathetic nerves peripherally and noradrenergic brainstem nuclei A1-A7 centrally. Peripheral norepinephrine has little influence on pain in healthy tissues, whereas in injured tissues it has variable effects, including aggravation of pain. Its peripheral pronociceptive effect has been associated with injury-induced expression of novel noradrenergic receptors, sprouting of sympathetic nerve fibers, and pronociceptive changes in the ionic channel properties of primary afferent nociceptors, while an interaction with the immune system may contribute in part to peripheral antinociception induced by norepinephrine. In the spinal cord, norepinephrine released from descending pathways suppresses pain by inhibitory action on alpha-2A-adrenoceptors on central terminals of primary afferent nociceptors (presynaptic inhibition), by direct alpha-2-adrenergic action on pain-relay neurons (postsynaptic inhibition), and by alpha-1-adrenoceptor-mediated activation of inhibitory interneurons. Additionally, alpha-2C-adrenoceptors on axon terminals of excitatory interneurons of the spinal dorsal horn possibly contribute to spinal control of pain. At supraspinal levels, the pain modulatory effect by norepinephrine and noradrenergic receptors has varied depending on many factors such as the supraspinal site, the type of the adrenoceptor, the duration of the pain and pathophysiological condition. While in baseline conditions the noradrenergic system may have little effect, sustained pain induces noradrenergic feedback inhibition of pain. Noradrenergic systems may also contribute to top-down control of pain, such as induced by a change in the behavioral state. Following injury or inflammation, the central as well as peripheral noradrenergic system is subject to various plastic changes that influence its antinociceptive efficacy.
Designing with flash memory (1993)

From the Publisher:
Since its introduction as a commercial product, flash memory has been adopted into a very broad range of applications, ranging from proprietary embedded systems to personal computers. Finally, a book has been written on this innovative technology, helping you master techniques for integrating it into your designs.
Here's where you'll get all of your flash-related questions answered: How does it work? What are the different types, and how do they differ? What is a flash file system? What special hardware and software do flash cards require? Learn detailed flash memory design principles. Become an expert in implementing and optimizing systems containing flash memory, whether used for embedded firmware or secondary mass storage.
Starting with the fundamentals, this book explains the read, write and erase mechanisms of the flash cell, including the software algorithms for the various flash memory technologies. Flash memory voltage generation and power consumption is another very important, and often overlooked, topic covered here.
This book sorts out the essential elements of a flash file system and provides an analysis of the different approaches in use today.
Learn how to implement the flash memory control signals and interpret AC timing waveforms. Discover what it takes to integrate flash cards into your PCMCIA or ExCA compatible systems, both from a hardware and a software standpoint (including a detailed explanation of Socket Services).
Designing with Flash Memory is the flash bible. If your job requires you to be up to date on the newest technology, you need this book now!
Assessing Different E3 Ligases for Small Molecule Induced Protein Ubiquitination and Degradation (2017)

Proteolysis targeting chimera (PROTAC) technology, the recruitment of E3 ubiquitin ligases to induce the degradation of a protein target, is rapidly impacting chemical biology, as well as modern drug development. Here, we explore the universality of this approach by evaluating different E3 ubiquitin ligases, engineered in their substrate binding domains to accept a recruiting ligand. Five out of six E3 ligases were found to be amenable to recruitment for target degradation. Taking advantage of the tight spatiotemporal control of inducing ubiquitination on a preselected target in living cells, we focused on two of the engineered E3 ligases, βTRCP and parkin, to unravel their ubiquitination characteristics in comparison with the PROTAC-recruited endogenous E3 ligases VHL and cereblon.
A novel 3D in vitro model of the human gut microbiota (2020)

Clinical trials and animal studies on the gut microbiota are often limited by the difficult access to the gut, restricted possibility of in vivo monitoring, and ethical issues. An easily accessible and monitorable in vitro model of the gut microbiota represents a valid tool for a wider comprehension of the mechanisms by which microbes interact with the host and with each other. Herein, we present a novel and reliable system for culturing the human gut microbiota in vitro. An electrospun gelatin structure was biofabricated as scaffold for microbial growth. The efficiency of this structure in supporting microbial proliferation and biofilm formation was initially assessed for five microbes commonly inhabiting the human gut. The human fecal microbiota was then cultured on the scaffolds and microbial biofilms monitored by confocal laser and scanning electron microscopy and quantified over time. Metagenomic analyses and Real-Time qPCRs were performed to evaluate the stability of the cultured microbiota in terms of qualitative and quantitative composition. Our results reveal the three-dimensionality of the scaffold-adhered microbial consortia that maintain the bacterial biodiversity and richness found in the original sample. These findings demonstrate the validity of the developed electrospun gelatin-based system for in vitro culturing the human gut microbiota.
Cerebrospinal fluid biomarkers in parkinsonian conditions: an update and future directions (2014)

Parkinsonian diseases comprise a heterogeneous group of neurodegenerative disorders, which show significant clinical and pathological overlap. Accurate diagnosis still largely relies on clinical acumen; pathological diagnosis remains the gold standard. There is an urgent need for biomarkers to diagnose parkinsonian disorders, particularly in the early stages when diagnosis is most difficult. In this review, several of the most promising cerebrospinal fluid candidate markers will be discussed. Their strengths and limitations will be considered together with future developments in the field.
Rheology and gelation kinetics in laponite dispersions containing poly(ethylene oxide) (2004)

Abstract We report results on the rheology of a model polymer/clay system, laponite clay particles with added poly(ethylene oxide) (PEO), focusing on the kinetics of gel formation and on molecular weight effects. We examined solutions at both pH = 7, where interparticle attractions are present and a networked gel is formed; and at pH = 10, where repulsive forces dominate and laponite forms a colloidal glass. We found that PEO of low to moderate molecular weight significantly slows down gelation and decreases the complex viscosity and elastic modulus of the dispersion by several orders of magnitude for both pH = 7 and 10. In the former case, adsorbed PEO likely forms a steric barrier to the formation of an attractive gel. In the latter case, we propose that free PEO chains in solution induce a depletion attraction between particles, preventing or slowing the formation of a colloidal glass. At higher molecular weights, PEO chains are long enough to bridge between particles and form an associative network, enhancing the viscosity and elastic modulus for both pH = 7 and 10. Finally, we have shown the critical molecular weight for transitioning between these two types of behavior scales with the interparticle distance. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 233–240, 2005
Hematoporphyrin derivative fluorescence: Photographic techniques for the localization of malignant tissue (1986)

Three simple methods for the detection of malignancy by the photography of hematoporphyrin derivative (HPD) fluorescence are presented. Two methods employ a single lens reflex camera with macrolens and Kodak high-speed Ektachrome (EL 400) film. Both employ a Corning Glass #3482 filter as a barrier on the lens. In method I, a single Kodak Wratten #39 filter is placed over a fluorescent "black light" source (two General Electric F20T12BL 20-W bulbs). In method II, twin electronic flash units (5,500 BCPS unfiltered) with a double thickness of Kodak Wratten #39 filter over them provide the light of excitation. Method III employs an adapted Polaroid SLR 680E Sun camera with two electronic flash units (5,500 BCPS, total unfiltered) rigged with a slave trigger. A Corning Glass #3482 filter is placed on the lens to act as a barrier, and two filters of Kodak Wratten #39 glass are placed on each flash unit. Photographs are taken in a darkened room.
Metabolic and structural evidence for the existence of a third species of polyphosphoinositide in cells: d-phosphatidyl-myo-inositol 3-phosphate (1989)

When human 1321 N1 astrocytoma cells were labelled to steady state with [3H]inositol and briefly with [32P]orthophosphate, a compound which contained both radiotracers and which co-migrated with phosphatidylinositol-myo-inositol 4-phosphate during t.l.c. could be extracted in acidic chloroform/methanol. Treatment with methylamine under conditions which lead to deacylation of conventional glycerophospholipids yielded a water-soluble moiety which was labelled with both radioisotopes and was eluted from an anion-exchange h.p.l.c. column with a retention time similar to, but distinct from, that of glycerophosphoinositol 4-phosphate. Experiments using sodium periodate and selective phosphatase enzymes to degrade this compound systematically generated a series of products which suggested the structure of the parent phospholipid was phosphatidyl-myo-inositol 3-phosphate (PtdIns3P). PtdIns3P is metabolically closely related to the pool(s) of inositol phospholipid(s) that serves as substrate(s) for an agonist-sensitive phosphoinositidase C, as the levels of PtdIns3P fell significantly when 1321 N1 cells were stimulated with carbachol. The relative rate of turnover of the inositol moiety of PtdIns3P is similar to that of both of the major polyphosphoinositides and significantly higher than that of total cellular phosphatidyl-myo-inositol. This suggests that all three polyphosphoinositides are synthesized from a common, rapidly metabolized, pool of phosphatidyl-myo-inositol.
Structural Chemistry and the Local Charge Picture of Copper Oxide Superconductors (1990)

The crystal structures of the known copper oxide superconductors are described, with particular emphasis on the manner in which they fall into structural families. The local charge picture, a framework for understanding the influence of chemical composition, stoichiometry, and doping on the electrical properties of complex structures, is also described.
An engineered Staphylococcus aureus PCI ß-lactamase that hydrolyses third-generation cephalosporins (1995)

The beta-lactamase from Staphylococcus aureus PC1 has been cloned into an Escherichia coli vector for site-directed mutagenesis and high-level protein expression. A mutant enzyme has been produced in which Ala238 is replaced by a serine, and Ile239 is deleted (A238S:I239del). The engineered enzyme hydrolyses third-generation cephalosporins substantially more rapidly than the parental enzyme does, while hydrolysis of benzylpenicillin is slower with the mutant than with the wild-type and native enzymes. The mutant beta-lactamase has been crystallized and the structure determined and refined at 2.8 A resolution. The disposition of the beta-strand which forms the side of the active site is altered in comparison with the native S. aureus beta-lactamase structure, widening the active site cleft and providing space to accommodate the bulky side-chains of the third-generation cephalosporins.