gebhart/patrepeval huggingface dataset:
Regularity and latency of units in ventral cochlear nucleus: implications for unit classification and generation of response properties (1988)

1. The responses of neurons in the ventral cochlear nucleus (VCN) of decerebrate cats are described with regard to their regularity of discharge and latency. Regularity is measured by estimating the mean and standard deviation of interspike intervals as a function of time during responses to short tone bursts (25 ms). This method extends the usual interspike-interval analysis based on interval histograms by allowing the study of temporal changes in regularity during transient responses. The coefficient of variation (CV), equal to the ratio of standard deviation to mean interspike interval, is used as a measure of irregularity. Latency is measured as the mean and standard deviation of the latency of the first spike in response to short tone bursts, with 1.6-ms rise times. 2. The regularity and latency properties of the usual PST histogram response types are shown. Five major PST response type classes are used: chopper, primary-like, onset, onset-C, and unusual. The presence of a prepotential in a unit's action potentials is also noted; a prepotential implies that the unit is recorded from a bushy cell. 3. Units with chopper PST histograms give the most regular discharge. Three varieties of choppers are found. Chop-S units (regular choppers) have CVs less than 0.35 that are approximately constant during the response; chop-S units show no adaptation of instantaneous rate, as measured by the inverse of the mean interspike interval. Chop-T units have CVs greater than 0.35, show an increase in irregularity during the response and show substantial rate adaptation. Chop-U units have CVs greater than 0.35, show a decrease in irregularity during the response, and show a variety of rate adaptation behaviors, including negative adaptation (an increase in rate during a short-tone response). Irregular choppers (chop-T and chop-U units) rarely have CVs greater than 0.5. Choppers have the longest latencies of VCN units; all three groups have mean latencies at least 1 ms longer than the shortest auditory nerve (AN) fiber mean latencies. 4. Chopper units are recorded from stellate cells in VCN (35, 42). Our results for chopper units suggest a model for stellate cells in which a regularly firing action potential generator is driven by the summation of the AN inputs to the cell, where the summation is low-pass filtered by the membrane capacitance of the cell.(ABSTRACT TRUNCATED AT 400 WORDS)
A tyrosine‐phosphorylated 110–120‐kDa protein associates with the C‐terminal SH2 domain of phosphotyrosine phosphatase‐1D in T cell receptor‐stimulated T cells (1996)

The role of cytosolic phosphotyrosine phosphatases (PTPase) in T cell receptor (TCR)-mediated signaling was investigated. PTPase activity was detected in a purified immunocomplex comprising aggregated TCR from the cell surface of Jurkat T cells. Since TCR aggregation results in phosphorylation of critical immunoreceptor tyrosine-based activation motifs (ITAM) in the TCR zeta chain, a doubly tyrosine-phosphorylated synthetic peptide containing the membrane-proximal zeta chain ITAM (zeta p ITAM) was used to characterize TCR zeta-associated PTPases. PTPase activity was detected in stable association with zeta p ITAM and the SH2 domain-containing PTPase PTP-1D (Syp, SH-PTP2) was identified in this complex. TCR stimulation resulted in increased total PTPase activity and PTP-1D protein in zeta p ITAM precipitates. TCR stimulation did not result in the tyrosine phosphorylation of PTP-1D but caused the rapid and transient tyrosine phosphorylation of a 110-120-kDa protein which associated selectively with the C-terminal SH2 domain of PTP-1D. This currently unidentified phosphotyrosine protein may be involved in localizing PTP-1D to the TCR following receptor stimulation.
Synthetic Pre-miRNA-Based shRNA as Potent RNAi Triggers (2011)

RNA interference (RNAi) is a powerful tool for studying gene function owing to the ease with which it can selectively silence genes of interest, and it has also attracted attention because of its potential for therapeutic applications. Chemically synthesized small interfering RNAs (siRNAs) and DNA vector-based short hairpin RNAs (shRNAs) are now widely used as RNAi triggers. In contrast to expressed shRNAs, the use of synthetic shRNAs is limited. Here we designed shRNAs modeled on a precursor microRNA (pre-miRNA) and evaluated their biological activity. We demonstrated that chemically synthetic pre-miRNA-based shRNAs have more potent RNAi activity than their corresponding siRNAs and found that their antisense strands are more efficiently incorporated into the RNA-induced silencing complex. Although greater off-target effects and interferon responses were induced by shRNAs than by their corresponding siRNAs, these effects could be overcome by simply using a lower concentration or by optimizing and chemically modifying shRNAs similar to synthetic siRNAs. These are challenges for the future.
Mechanisms that regulate the production and effects of tumor necrosis factor-alpha. (1989)

Macrophage-derived tumor necrosis factor (TNF) is increasingly being recognized as an important monokine possessing multifunctional activities. Current evidence has demonstrated that TNF can induce a number of pleomorphic effects in both physiological and immunological systems. Historically, the biological effects and nomenclature of TNF centered around the induction of hemorrhagic necrosis of specific solid murine tumors. This effected function has been greatly expanded upon, and TNF is now recognized as an important peptide mediator involved in various facets of cell activation. This is exemplified by the central role that TNF plays in endotoxemia, shock and multiple organ failure syndromes. Although TNF has been incriminated as the molecular signal mediating number of pathophysiological derangements, the regulatory mechanisms that control TNF expression at the cellular and molecular levels, as well as the modulation of the in vivo activity of preformed TNF, has not been full addressed. In this review, a detailed description of the mechanisms that regulate the production and effects of TNF is presented.
1,2,4-Triazine Analogs of the Natural Pyrimidines (1956)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT1,2,4-Triazine Analogs of the Natural PyrimidinesElvira A. Falco, Elizabeth Pappas, and George H. HitchingsCite this: J. Am. Chem. Soc. 1956, 78, 9, 1938–1941Publication Date (Print):May 1, 1956Publication History Published online1 May 2002Published inissue 1 May 1956https://pubs.acs.org/doi/10.1021/ja01590a047https://doi.org/10.1021/ja01590a047research-articleACS PublicationsRequest reuse permissionsArticle Views334Altmetric-Citations32LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
ChemInform Abstract: Why Pentose‐ and Not Hexose‐Nucleic Acids? Part 4. Homo‐DNA: 1H, 13C, 31P, and 15N NMR Spectroscopic Investigation of ddGlc(A‐A‐A‐A‐A‐T‐T‐T‐ T‐T) in Aqueous Solution. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Biochemical characterization of Anabaena sp. strain PCC 7120 non‐specific nuclease NucA and its inhibitor NuiA (1998)

We have established overexpression systems and purification protocols for NucA and NuiA, a sugar non-specific nuclease and its protein inhibitor from Anabaena sp. strain PCC 7120, in order to characterize these proteins in detail. CD spectroscopy revealed that NucA has a similar secondary-structure composition, 13% alpha helix and 20% beta sheet, to the related Serratia nuclease, while NuiA represents a protein with a higher alpha-helical (29%) and beta-sheet (24%) content than NucA. Denaturation experiments showed that the stabilities of NucA and NuiA are in the typical range for proteins of mesophilic organisms, NuiA with deltaG0H2O = 63.4 J x mol(-1)residue, being slightly more stable than its target NucA with delta deltaG0H2O = 46.3 J x mol(-1)residue. The nuclease requires divalent metal ions as cofactors, the optimum concentration being around 5 mM for Mn2+ or Mg2+. The order of effectiveness of various divalent cations to function as cofactors for the hydrolytic activity of NucA is Mn2+ = Co2+ > Mg2+ > or = Ni2+ >> or Ca2+ = Cd2+ at a concentration of 5 mM. Nuclease activity decreases with increasing concentration of monovalent salt. The activity of NucA shows a pH optimum at pH 5.5-7.5. The temperature optimum is around 35 degrees C, the activation energy was calculated to be 53 kJ mol(-1). The specific activity of the nuclease towards high molecular-mass DNA is 8.4 x 10(6) Kunitz-units x mg(-1), which means that NucA is one of the most active nucleases known. Kinetic constants for the cleavage of various DNA and RNA substrates by NucA are all in the range Km < or = 0.1 mg x ml(-1) and k(cat) approximately 1000 s(-1). As other non-specific nucleases, NucA exhibits sequence preferences, similar to the related Serratia nuclease, NucA avoids cleavage of d(A) x d(T) tracts. The nucleolytic activity of NucA is completely inhibited at equimolar concentrations of nuclease and inhibitor. An ultracentrifugation analysis showed that NucA and NuiA form a 1:1 complex. The interaction of NucA with NuiA was also investigated by CD spectroscopy and revealed no major conformational changes upon complex formation of the two proteins.
Macrophage migration inhibitory factor is a critical mediator of the activation of immune cells by exotoxins of Gram-positive bacteria (1998)

Discovered in the early 1960s as a T cell cytokine, the protein mediator known as macrophage migration inhibitory factor (MIF) has been found recently to be a pituitary peptide released during the physiological stress response, a proinflammatory macrophage cytokine secreted after LPS stimulation, and a T cell product expressed as part of the antigen-dependent activation response. We report herein that MIF also plays a critical role in the innate host response to staphylococcal and streptococcal exotoxins. In RAW 264.7 or elicited mouse peritoneal macrophages, peak MIF secretion was induced by concentrations of the staphylococcal toxic shock syndrome (TSS) toxin 1 (TSST-1) and the streptococcal pyrogenic exotoxin A as low as 10 pg/ml. Moreover, dose-response studies of splenocyte cytokine production showed that lower concentrations of TSST-1 (10 pg/ml) were needed to release MIF than to induce interleukin 2 or interferon-gamma secretion (1 ng/ml). We also studied the effect of neutralizing anti-MIF antibodies on TSST-1-induced lymphocyte proliferation and lethal toxic shock. Pretreatment of C57BL/6 mice with anti-MIF antibody 2 hr before TSST-1 injection prevented spleen enlargement and reduced by 50% the proliferation of splenocytes measured ex vivo. In a lethal mouse model of TSST-1-induced shock, anti-MIF antibody increased survival from 8% to 54% (P < 0.0001). These studies indicate that Gram-positive exotoxins are extremely potent inducers of MIF secretion and establish a critical role for MIF and the macrophage in the pathogenesis of the TSSs and in the innate immune response.
Inhibition of human immunodeficiency virus in early infected and chronically infected cells by antisense oligodeoxynucleotides and their phosphorothioate analogues. (1989)

Antisense oligodeoxynucleotides, both the phosphorothioate analogues and unmodified oligomers of the same sequence, inhibit replication and expression of human immunodeficiency virus already growing in tissue cultures of MOLT-3 cells with much greater efficacy than do mismatched ("random") oligomers and homooligomers of the same length and with the same internucleotide modification. This preferential inhibitory effect is elicited in as short a time as 4-24 hr postinfection. Likewise, antisense oligomers exhibit greater inhibitory effects on human immunodeficiency virus in chronically infected cells than do mismatched oligomers and homooligomers. Phosphorothioate antisene oligomers are up to 100 times more potent than unmodified oligomers of the same sequence in these inhibitory assays. These results, in major respects, confirm and extend those recently published by Matsukura et al. [Matsukura, M., Zon, G., Shinozuka, K., Robert-Guroff, M., Shimada, T., Stein, C. A., Mitsuza, H., Wong-Staal, F., Cohen, J. S. & Broder, S. (1989) Proc. Natl. Acad. Sci. USA 86, 4244-4248]. They also point out the importance of computer analysis of sequences though to be random but that in reality contain significant areas of likely hybridization, either to the viral genome or to the complementary DNA strand synthesized from it. They thus reinforce the concept that specific base pairing is a crucial feature of oligonucleotide inhibition of human immunodeficiency virus.
Electrical, thermoelectric, and optical properties of strongly degenerate polycrystalline silicon films (1984)

Low-pressure chemical vapor deposited polycrystalline silicon films 0.45 μm thick were doped to strongly degenerate concentrations (1–2×1020 cm−3) by thermal diffusion of phosphorus. Thermoelectric power, Hall effect, and resistivity measurements were made over the temperature range of 80 to 340 K. The thermopower results were in good agreement with single crystal degenerate semiconductor theory. Additionally, these results, in conjunction with the measured carrier concentration, showed that the scattering relaxation time is inversely proportional to the square root of the carrier energy which is indicative of lattice scattering. The temperature dependence of the resistivity was found to be of the form ρ=a+bT. The liner term was attributed to acoustic phonon scattering within the grains and the constant term to lattice mismatch at the grain boundaries. Scattering from grain boundary potential barriers due to carrier trapping appeared to play no significant role although this effect dominates at lower doping concentrations. The index of refraction and absorption coefficient in the near infrared and visible were determined from transmission and reflection measurements of doped and undoped polycrystalline silicon films on quartz substrates.
Use of coherent control for selective two-photon fluorescence microscopy in live organisms (2006)

We demonstrate selective fluorescence We demonstrate selective fluorescence excitation of specific molecular species in live organisms by using coherent control of two-photon excitation. We have acquired quasi-simultaneous images in live fluorescently-labeled Drosophila embryos by rapid switching between appropriate pulse shapes. Linear combinations of these images demonstrate that a high degree of fluorophore selectivity is attainable through phase-shaping. Broadband phase-shaped excitation opens up new possibilities for single-laser, multiplex, in-vivo fluorescence microscopy.
A Comparison of the Kernel Equating Method with Traditional Equating Methods Using SAT® Data (2008)

This study applied kernel equating (KE) in two scenarios: equating to a very similar population and equating to a very different population, referred to as a distant population, using SAT ® data. The KE results were compared to the results obtained from analogous traditional equating methods in both scenarios. The results indicate that KE results are comparable to the results of other methods. Further, the results show that when the two populations taking the two tests are similar on the anchor score distributions, different equating methods yield the same or very similar results, even though they have different assumptions.
An ultraviolet light-damaged DNA recognition protein absent in xeroderma pigmentosum group E cells binds selectively to pyrimidine (6–4) pyrimidone photoproducts (1992)

The binding specificity was defined of a human ultraviolet light-damaged DNA recognition protein (UV-DRP), the activity of which is absent in some xeroderma pigmentosum complementation group E cells. Our results suggest that cyclobutane pyrimidine dimers (CPDs) are not high affinity UV-DRP binding sites--a finding consistent with other reports on this protein (Hirschfeld et al., (1990) Mol. Cell Biol., 10, 2041-2048). A major role for 6-4 photoproducts in UV-DRP binding was suggested in studies showing that irradiated oligonucleotides containing a T4C UV box sequence, which efficiently forms a TC 6-4 photoproduct, was a superior substrate for the UV-DRP when compared to a similar irradiated oligonucleotide having a T5 sequence. The latter sequence forms CPDs at a much higher frequency than 6-4 photoproducts. In a more direct approach, T4C-containing oligonucleotides complexed with the UV-DRP were separated from the unbound oligonucleotide fraction and the frequencies of 6-4 photoproducts in the two DNA populations were compared. The UV-DRP-bound fraction was highly enriched for the 6-4 lesion over the unbound fraction supporting the conclusion that 6-4 photoproducts are the principal binding cues for the UV-DRP.
Organic light emitting diodes and photodetectors: Toward applications in lab-on-a-chip portable devices (2005)

We report that polymer light emitting diodes (pLEDs) and polymer photodetectors can be integrated on disposable polydimethylsiloxane [PDMS] microfluidic flowcells to form hybrid microchips for bioluminescence applications. PLEDs were successfully employed as excitation light sources for microchip based fluorescence detection of microalbuminuria (MAU), an increased urinary albumin excretion indicative of renal disease. To circumvent the use of optical filters, fluorescence was detected perpendicular to the biolabel flow direction using a CCD spectrophotometer. Prior to investigating the suitability of polymer photodiodes as integrated detectors for fluorescence detection, their sensitivity was tested with on-chip chemiluminescence. The polymer photodetector was integrated with a PDMS microfluidic flowcell to monitor peroxyoxalate based chemiluminescence (CL) reactions on the chip. This work demonstrates that our polymer photodetectors exhibit sensitivities comparable to inorganic photodiodes. Here we prove the concept that thin film solution-processed polymer light sources and photodetectors can be integrated with PDMS microfluidic channel structures to form a hybrid microchip enabling the development of disposable low-cost diagnostic devices for point-of-care analysis.
Amphiphilic Bicyclic Peptides as Cellular Delivery Agents (2014)

Two bicyclic peptides composed of tryptophan and arginine residues were synthesized from monocyclic peptide building blocks and evaluated as cellular delivery agents. [W5G]-(triazole)-[KR5] and [W5E]-(β-Ala)-[KR5] containing triazole and β-alanine linkers improved the cellular delivery of fluorescein (F')-labeled phosphopeptide F'-GpYEEI (F'-PP) by 7.6- and 19.3-fold, respectively, in human ovarian adenocarcinoma cells. However, parent monocyclic peptide [R5 ] and monocyclic peptide [WR]4 only enhanced the cellular uptake of the phosphopeptide by only 1.3- and 3.7-fold, respectively. Confocal microscopy showed that the corresponding fluorescein-labeled bicyclic peptide F'-[KW4E]-(β-Ala)-[KR5] was localized in the cytosol and nucleus. Studying the cellular uptake of F'-[KW4E]-(β-Ala)-[KR5] in the presence of endocytosis inhibitors indicated that the clathrin- and caveolin-dependent endocytosis are the main pathways for cellular uptake. The bicyclic peptide was able to improve antiproliferative activity of doxorubicin by 20 %. These data suggest that this bicyclic peptide can be utilized as a new class of cell-penetrating peptides and cellular delivery tools.
Effect of Alipogene Tiparvovec (AAV1-LPLS447X) on Postprandial Chylomicron Metabolism in Lipoprotein Lipase-Deficient Patients (2012)

Intramuscular administration of alipogene tiparvovec resulted in a significant improvement of postprandial chylomicron metabolism in LPLD patients, without inducing large postprandial NEFA spillover.
Duration of effect of intravenous antibiotics on spirometry and sputum cytokines in children with cystic fibrosis (2003)

Intravenous (IV) antibiotics are a mainstay of therapy in children with cystic fibrosis. It is unclear, however, over what period associated improvements in pulmonary function are maintained, and to what extent the underlying inflammatory process is impeded in children admitted for a course of IV antibiotics. This was a prospective, interventional study of 14 children (median age, 14 years; interquartile range, 10-14) with cystic fibrosis who were regular sputum producers and who required admission for a 2-week course of IV antibiotics. Children performed spirometry and provided a sputum sample prior to starting IV antibiotics and then weekly for 6 weeks, the first 2 weeks of which IV antibiotics were given. Sputum IL-8, TNF-alpha, IL-6, IL-10, MIP1-alpha, and elastase were measured. Seven children were asked to repeat the protocol in a subsequent exacerbation to assess similarities in response to therapy. Significant improvements were seen in forced expired volume in 1 sec (FEV(1)) in association with IV antibiotics (27% relative improvement in predicted from baseline to end of week 1, median FEV(1) 41.3% increasing to 52.2%), but this continued only 1 week following cessation of antibiotics. Although IL-8 demonstrated a trend for reduction in association with antibiotics, no significant profile was demonstrated for any of the cytokines assessed. IL-10 was detectable in 64% of samples (all <100 pg/ml). In children with two episodes assessed, although there was a close correlation of FEV(1) and FVC between exacerbations (before antibiotics), no significant correlation was seen for IL-8, TNF-alpha, or IL-10 measured in both sets of samples at any sample point (indeed, a discordant response was seen between sample points in the two exacerbations). Although FEV(1) temporarily improves in response to admission for IV antibiotics, no such response is seen in sputum cytokine values. In addition, assessment of cytokines in subsequent exacerbations does not show a similar pattern of response to treatment.
Chronic Canine Ehrlichiosis (Ehrlichia canis): A Retrospective Study of 19 Natural Cases (2004)

Nineteen dogs from Greece with chronic ehrlichiosis were studied. The dogs exhibited bicytopenia or pancytopenia, bone marrow hypoplasia, seroreactivity to Ehrlichia canis (E. canis) antigens, and had no history of drug or radiation exposure. Anorexia, depression, severe bleeding tendencies, hypoalbuminemia, and increased serum alanine aminotransferase activity were also hallmarks of the disease. All these animals eventually died, irrespective of the treatment applied. Some dogs were also serologically positive for Rickettsia conorii, Leishmania infantum (L. infantum), and Bartonella vinsonii subspp. berkhoffii. Polymerase chain reaction testing of bone marrow samples revealed E. canis, Anaplasma phagocytophilia, Anaplasma platys, and L. infantum in some dogs. Concurrent infections did not appear to substantially influence the clinical course and final outcome of the chronic canine ehrlichiosis.