gebhart/patrepeval huggingface dataset:
Prokaryotic silencing (psi)RNAs inPyrococcus furiosus (2008)

In many prokaryotes, noncoding RNAs that arise from the clustered regularly interspaced short palindromic repeat (CRISPR) loci are now thought to mediate defense against viruses and other molecular invaders by an RNAi-like pathway. CRISPR loci contain multiple short regions of similarity to invader sequences separated by short repeat sequences, and are associated with resistance to infection by corresponding viruses. It is hypothesized that RNAs derived from these regions, termed prokaryotic silencing (psi)RNAs, guide Slicer-like complexes of partner proteins to destroy invader nucleic acids. Here we have investigated CRISPR-derived RNAs in the archaeon Pyrococcus furiosus. Northern analysis revealed multiple RNA species consistent with a proposed biogenesis pathway that includes full-length CRISPR locus transcripts and intermediates generated by endonucleolytic cleavages within the repeat sequences. However, our results identify the principal products of the CRISPR loci as small psiRNAs comprised primarily of invader-targeting sequence with perhaps only 5-10 nucleotides of CRISPR repeat sequence. These RNAs are the most abundant CRISPR RNA species in P. furiosus and are likely the guides for the effector complexes of the proposed prokaryotic RNAi (pRNAi) system. We analyzed cell-free extracts fractionated under non-denaturing conditions and found that the various CRISPR RNA species are components of distinct RNA-protein complexes, including at least two complexes that contain mature-length psiRNAs. Finally, RNAs are produced from all seven CRISPR loci present in the P. furiosus genome, and interestingly, the most recently acquired psiRNAs encoded proximal to the leader sequence of a CRISPR locus appear to be the most abundant.
Stealth and Cunning: Hepatitis B and Hepatitis C Viruses (2005)

Collectively, the results summarized in this review suggest that HBV acts like a stealth virus early in infection, remaining undetected and spreading until the onset of the adaptive immune response several weeks later. We suspect that the relative invisibility of HBV to the innate sensing machinery of the cells reflects its replication strategy, which sequesters the transcriptional template in the nucleus, entails the production of capped and polyadenylated viral mRNAs that resemble the structure of normal cellular transcripts, and the replicating viral genome is sheltered within viral capsid particles in the cytoplasm and, therefore, does not elicit a response. In contrast, HCV activates a strong intracellular antiviral response in the liver, presumably because it replicates via a dsRNA intermediate in the cytoplasm, where it can readily induce the cellular dsRNA sensing apparatus and initiate the signaling cascade. In turn, this results in the induction of many genes, such as the 2′,5′-oligoadenylate synthetase Mx1, that have known antiviral activity (reviewed in references 128 and 141); TRIM14 and 22, members of the same gene family as TRIM5, which has been shown to be part of the host defense against retroviruses (reviewed in reference 11); and ISG15, which has recently been proposed to have a role in innate immunity (124). Impressively, however, HCV cunningly manages to spread through the liver despite induction of these genes, presumably because its E2, NS3, and NS5A proteins can defeat them. On the other hand, both viruses can be controlled when CD8+ T cells enter the liver, recognize antigen, kill whatever infected cells they encounter, and secrete IFN-γ, which triggers a broad-based cascade that amplifies the inflammatory process and has antiviral activity, at least in HBV-transgenic mice and the HBV and HCV cell culture systems. The unexpected finding that HBV does not modulate host cellular gene transcription and apparently does not induce an innate immune response when spreading through the liver raises the possibility that HBV, unlike HCV and other viruses, has evolved to evade innate immunity by not inducing it rather then actively counteracting it; this, in turn, might leave HBV very sensitive to intracellular antiviral mechanisms when they are induced by the adaptive immune system or an unrelated viral infection. Although we suggest that HBV and HCV infections can be inhibited noncytopathically by the cellular genes that are induced during this process, the identities of those genes, the antiviral mechanisms they elicit, and the unique evasion strategies of each virus remain to be determined, marking a new starting point in the quest to understand the cellular and molecular immunobiology of these viral infections.
Functional Relationships of the Genetic Locus Encoding the Glycosyltransferase Enzymes Involved in Expression of the Lacto-N-neotetraose Terminal Lipopolysaccharide Structure in Neisseria meningitidis (1996)

The biosynthetic function of the lgtABE genetic locus of Neisseria meningitidis was determined by structural analysis of lipopolysaccharide (LPS) derived from mutant strains and enzymic assay for glycosyltransferase activity. LPS was obtained from mutants generated by insertion of antibiotic resistance cassets in each of the three genes lgtA, lgtB, lgtE of the N. meningitidis immunotype L3 strain phi3 MC58. LPS from the parent strain expresses the terminal lacto-N-neotetraose structure, Galbeta1-->4GlcNAcbeta1-->3Galbeta1-->4Glc. Mild hydrazine treatment of the LPS afforded O-deacylated samples that were analyzed directly by electrospray ionization mass spectrometry (ESI-MS) in the negative ion mode. In conjunction with results from sugar analysis, ESI-MS revealed successive loss of the sugars Gal, GlcNAc, and Gal in lgt B, lgt A, and lgt E LPS, respectively. The structure of a sample of O- and N-deacylated LPS derived by aqueous KOH treatment of lgt B LPS was determined in detail by two-dimensional homo- and heteronuclear NMR methods. Using a synthetic beta-GlcNAc acceptor and a beta-lactose acceptor, the glycosyltransferase activities encoded by the lgtB and lgtA genes were unambiguously established. These data provide the first definitive evidence that the three genes encode the respective glycosyltransferases required for biosynthesis of the terminal trisaccharide moiety of the lacto-N-neotetraose structure in Neisseria LPS. From ESI-MS data, it was also determined that the Gal-deficient LPS expressed by the lgt E mutant is identical to that of the major component expressed by immunotype L3 galE-deficient strains. The galE gene which encodes for UDP-glucose-4-epimerase plays an essential role in the incorporation of Gal into meningococcal LPS.
Purinergic signalling: past, present and future (2008)

The discovery of non-adrenergic, non-cholinergic neurotransmission in the gut and bladder in the early 1960's is described as well as the identification of adenosine 5'-triphosphate (ATP) as a transmitter in these nerves in the early 1970's. The concept of purinergic cotransmission was formulated in 1976 and it is now recognized that ATP is a cotransmitter in all nerves in the peripheral and central nervous systems. Two families of receptors to purines were recognized in 1978, P1 (adenosine) receptors and P2 receptors sensitive to ATP and adenosine diphosphate (ADP). Cloning of these receptors in the early 1990's was a turning point in the acceptance of the purinergic signalling hypothesis and there are currently 4 subtypes of P1 receptors, 7 subtypes of P2X ion channel receptors and 8 subtypes of G protein-coupled receptors. Both short-term purinergic signalling in neurotransmission, neuromodulation and neurosecretion and long-term (trophic) purinergic signalling of cell proliferation, differentiation, motility, death in development and regeneration are recognized. There is now much known about the mechanisms underlying ATP release and extracellular breakdown by ecto-nucleotidases. The recent emphasis on purinergic neuropathology is discussed, including changes in purinergic cotransmission in development and ageing and in bladder diseases and hypertension. The involvement of neuron-glial cell interactions in various diseases of the central nervous system, including neuropathic pain, trauma and ischemia, neurodegenerative diseases, neuropsychiatric disorders and epilepsy are also considered.
Role of tumor necrosis factor and gamma interferon in acquired resistance to Cryptococcus neoformans in the central nervous system of mice (1995)

Although naive C.B-17 and BALB/cBy mice die of meningoencephalitis within 5 weeks of intravenous infection with an opportunistic strain of Cryptococcus neoformans, immunized mice express an acquired, CD4+ T-cell-dependent immunity and survive an intravenous infection. Infusion of lymphocytes from immune mice into severe combined immunodeficiency (SCID) mice renders these mice more resistant to cryptococcal brain infection than uninfused controls. We have investigated the role of gamma interferon (IFN-gamma) and tumor necrosis factor (TNF) in acquired resistance to C. neoformans. Neutralization of either IFN-gamma or TNF impaired resistance of immune BALB/cBy or C.B-17 mice to cryptococci. At 10 days postinfection, there were approximately 10 times as many yeast cells in the brains of mice treated with either anticytokine antibody as in the brains of mice treated with control antibody. Simultaneous neutralization of IFN-gamma and TNF further exacerbated infection. Neutralization of IFN-gamma or TNF also impaired resistance in immune lymphocyte-infused SCID mice, resulting in significantly higher yeast burdens in brains of cytokine-neutralized mice than in brains of controls. Concurrent neutralization of IFN-gamma and TNF rendered SCID recipients of immune cells equivalent to uninfused SCID mice with respect both to brain yeast burdens at 10 days and to survival. Anti-TNF treatment alone also curtailed survival. Histological examination of the brains of cytokine-neutralized mice revealed deficiencies in ability to focus inflammatory cells at brain lesions. These data demonstrate that both IFN-gamma and TNF are important mediators of acquired resistance to cryptococcal meningoencephalitis.
Nuclear-Cytoplasmic Interactions during the First Cell Cycle of Nuclear Transfer Reconstructed Bovine Embryos: Implications for Deoxyribonucleic Acid Replication and Development1 (1993)

The present study investigated the decay of maturation-promoting factor (MPF) activity in electrically activated in vitro-matured bovine oocytes and examined the influence of the cell cycle stage of both the donor nucleus and the recipient cytoplasm upon the morphology and DNA synthesis potential of the donor nucleus in reconstructed embryos. The decay of MPF activity was studied both biochemically in electrically activated in vitro-matured oocytes and by morphological examination of nuclear structure in reconstructed bovine embryos. As measured by H1 kinase activity in groups of 10 oocytes, the level of MPF declined rapidly to 30 +/- 4% (of the maximum level in unactivated control oocytes) at 60 min and reached a basal level of 20 +/- 6% at 120 min. This level of activity was then maintained until at least 9 h postactivation. In contrast, when MPF activity was assayed by morphological examination of nuclei in individual reconstructed embryos, the decline in activity occurred over a period of 9 h postactivation. DNA synthesis of nuclei arrested at the G1/S border and in G2 phases of the cell cycle was examined in embryos reconstructed at the time of oocyte activation, i.e., when MPF levels were maximal, and by fusion 10 h postactivation, when no MPF activity could be detected. All nuclei transferred at the time of oocyte activation underwent nuclear envelope breakdown (NEBD) and subsequent DNA synthesis. However, when nuclei were transferred 10 h after activation, no NEBD was observed in any nuclei. Nuclei arrested at the G1/S border or nuclei in S phase when transferred in the absence of NEBD underwent DNA synthesis, while no DNA synthesis was observed in G2 nuclei transferred into this cytoplasmic environment. The results presented show that all nuclei, regardless of cell cycle stage, undergo DNA replication when transplanted into metaphase II (MeII) cytoplasts in which MPF activity is high. From these observations we would suggest that one factor that may contribute to the present low frequency of development of bovine nuclear transfer embryos is the ploidy of the reconstructed embryo after the first cell cycle. In order to maintain correct ploidy of the reconstructed embryo, only G1 nuclei should be transferred at the time of activation, when MPF levels are high. In contrast, when the integrity of the nuclear membrane is maintained by transfer at 10 h postactivation, when MPF activity is absent, the rereplication of G2 nuclei is prevented and correct ploidy of the reconstructed embryo may be maintained.
Estimation of input function and kinetic parameters using simulated annealing: application in a flow model (2002)

Accurate determination of the input function is essential for absolute quantification of physiological parameters in positron emission tomography and single-photon emission computed tomography imaging, but it requires an invasive and tedious procedure of blood sampling that is impractical in clinical studies. We previously proposed a technique that estimates simultaneously kinetic parameters and the input function from the tissue impulse response functions and requires two blood samples. A nonlinear least squares method estimated all the parameters in the impulse response functions and the input function but failed occasionally due to high noise levels in the data, causing an ill-conditioned cost function. This paper investigates the feasibility of applying a Monte Carlo method called simulated annealing to estimate kinetic parameters in the impulse response functions and the input function. Time-activity curves of teboroxime, which is very sensitive to changes in the input function, were simulated based on published data obtained from a canine model. The equations describing the tracer kinetics in different regions were minimized simultaneously by simulated annealing and nonlinear least squares. We found that the physiological parameters obtained with simulated annealing are accurate, and the estimated input function more closely resembled the simulated curve. We conclude that simulated annealing reduces bias in the estimation of physiological parameters and determination of the input function.
Isolated Loss of PMS2 Expression in Colorectal Cancers: Frequency, Patient Age, and Familial Aggregation (2005)

Overall, 97% of the MSI-H tumors showed loss of expression for one or more of these four mismatch repair proteins. Selective loss of expression of PMS2 was present in 72% of cases in which colorectal cancers had an MSI-H phenotype but no alteration of expression of MLH1, MSH2, and MSH6. The underlying mechanism involved cannot be determined from this study but could involve point mutations in other DNA mismatch repair genes with retention of immunohistochemical expression, somatic inactivation of PMS2, or germ line mutation of PMS2.
CMS's Landmark Decision on CT Colonography — Examining the Relevant Data (2009)

In an unprecedented endorsement of evidence-based medicine, the Centers for Medicare and Medicaid Services (CMS) recently decided to deny coverage of computed tomographic (CT) colonography for cancer screening, concluding that “the evidence is inadequate.”1 The CMS emphasized that the “pivotal, overarching concern” in its decision was the fact that the findings of trials showing a benefit of screening with this method were not necessarily generalizable from the study populations to other groups of patients. In particular, the CMS noted that the mean age of participants in the studies that were cited in support of coverage was significantly lower than that . . .
Large-scale gene trapping in C57BL/6N mouse embryonic stem cells (2008)

We report the construction and analysis of a mouse gene trap mutant resource created in the C57BL/6N genetic background containing more than 350,000 sequence-tagged embryonic stem (ES) cell clones. We also demonstrate the ability of these ES cell clones to contribute to the germline and produce knockout mice. Each mutant clone is identified by a genomic sequence tag representing the exact insertion location, allowing accurate prediction of mutagenicity and enabling direct genotyping of mutant alleles. Mutations have been identified in more than 10,000 genes and show a bias toward the first intron. The trapped ES cell lines, which can be requested from the Texas A&M Institute for Genomic Medicine, are readily available to the scientific community.
Dephosphorylation of Endothelial Nitric-oxide Synthase by Vascular Endothelial Growth Factor (2002)

The endothelial isoform of nitric-oxide synthase (eNOS) is a key determinant of vascular tone. eNOS, a Ca(2+)/camodulin-dependent enzyme, is also regulated by a variety of agonist-activated protein kinases, but the role and regulation of the protein phosphatase pathways involved in eNOS dephosphorylation are much less well understood. Treatment of endothelial cells with vascular endothelial growth factor (VEGF), a potent eNOS agonist, leads to the activation of calcineurin, a Ca(2+)/camodulin-dependent protein phosphatase. In these studies, we used a phosphorylation state-specific antibody to show that VEGF promotes dephosphorylation of eNOS at serine residue 116 in cultured endothelial cells. Cyclosporin A, an inhibitor of calcineurin, completely blocks VEGF-induced eNOS dephosphorylation; under identical conditions, cyclosporin A also inhibits VEGF-induced eNOS activation. VEGF-induced eNOS dephosphorylation shows an EC(50) of 2 ng/ml and is maximal 30 min after agonist addition. eNOS phosphorylation at serine 116 is completely blocked by the protein kinase C inhibitor calphostin but is blocked by neither wortmannin (an inhibitor of phosphatidylinositide 3-kinase) nor the MAP kinase pathway inhibitor U0126. A phosphorylation-deficient mutant of eNOS in which serine 116 is changed to an alanine residue (S116A) shows significantly enhanced enzyme activity compared with the wild-type enzyme. Taken together, these findings indicated that VEGF-induced eNOS dephosphorylation at serine 116 leads to enzyme activation. Cyclosporin A is widely used as an immunosuppressive drug for which hypertension is an important dose-limiting side effect. Our results suggest that cyclosporin A-induced hypertension may involve, at least in part, the attenuation of endothelium-derived NO production through a calcineurin-sensitive pathway regulating eNOS dephosphorylation.
Modernization of Agriculture in Developing Countries: Resources, Potentials and Problems, Second Edition by Isaac Arnon. (Environmental Monographs & Symposia, Convener & General Editor Nicholas Polunin.) John Wiley & Sons, Baffins Lane, Chichester, Sussex P019 1UD, England, UK: xxiii + 626 pp., illustr., 23.5 × 16 × 4.25 cm, hard cover £60 or US $130, 1987. (1989)

Modernization of Agriculture in Developing Countries: Resources, Potentials and Problems, Second Edition by Isaac Arnon. (Environmental Monographs &amp; Symposia, Convener &amp; General Editor Nicholas Polunin.) John Wiley &amp; Sons, Baffins Lane, Chichester, Sussex P019 1UD, England, UK: xxiii + 626 pp., illustr., 23.5 × 16 × 4.25 cm, hard cover £60 or US $130, 1987. - Volume 16 Issue 3
Stealth viruses as neuropathogens. (1994)

Neuropsychiatric diseases viewed as multifaceted expression of a dysfunctional brain in which atypical responses are evoked by various sensory inputs. Disease entities have traditionally been classified according to the predominant manifestation ( ) without regard to the overlapping features of many of the diseases (+/-). Thus, mild to moderate pain, mood, cognitive, and neurosomatic symptoms are frequently present in chronic fatigue syndrome (CFS) patients. Fibromyalgia syndrome (FMS) is listed as an example of a predominantly chronic pain syndrome. Affect (mood) disorders include depression (Depress.), anxiety, panic reactions, blunted affect, mania, etc. Schizophrenia (Schizo.) is listed as an example of a major cognitive psychosis. Autism as well as various forms of dementia would be included in this category. Irritable bowel syndrome (IBS) is an example of a neurosomatic disease.
Transformative Evolution of Organolead Triiodide Perovskite Thin Films from Strong Room-Temperature Solid–Gas Interaction between HPbI3-CH3NH2 Precursor Pair (2016)

We demonstrate the feasibility of a nonsalt-based precursor pair--inorganic HPbI3 solid and organic CH3NH2 gas--for the deposition of uniform CH3NH3PbI3 perovskite thin films. The strong room-temperature solid-gas interaction between HPbI3 and CH3NH2 induces transformative evolution of ultrasmooth, full-coverage perovskite thin films at a rapid rate (in seconds) from nominally processed rough, partial-coverage HPbI3 thin films. The chemical origin of this behavior is elucidated via in situ experiments. Perovskite solar cells, fabricated using MAPbI3 thin films thus deposited, deliver power conversion efficiencies up to 18.2%, attesting to the high quality of the perovskite thin films deposited using this transformative process.
The Tumor-Associated Antigen PRAME Is Universally Expressed in High-Stage Neuroblastoma and Associated with Poor Outcome (2004)

PRAME expression in neuroblastoma is extraordinarily common and was universally seen in patients with advanced-stage disease in our study. Furthermore, significant impact of PRAME expression on the outcome of patients was shown. Thus, PRAME may present a particularly attractive target for immunotherapeutic strategies in neuroblastoma.
Cryptosporidium infection in Oregon public health clinic patients 1985-88: the value of statewide laboratory surveillance. (1990)

To evaluate the utility of statewide laboratory Cryptosporidium surveillance, we screened stools from all 5,256 patients evaluated at local health departments for parasitic disease from January 1985 through June 1988. Fifty-seven patients (1.1 percent) were found to have Cryptosporidium. Seasonal peaks in positivity were observed in the spring, summer, and early autumn months. In children, younger age was associated with higher positivity rate of cryptosporidiosis. As a result of these surveillance efforts, Oregon's first known outbreak of cryptosporidiosis was detected and investigated during 1988. Twenty-five persons were infected, including children, parents, and staff associated with two day care centers. The cost of routine screening for Cryptosporidium was $1.13 per specimen in our laboratory, and we consider it useful.