gebhart/patrepeval huggingface dataset:
Quantitative evaluation of intracellular sense: antisense RNA hybrid deuplexes (1993)

Previous studies have demonstrated that for an antisense RNA to be effective in attenuating gene expression, a large but indeterminate excess of antisense RNA is required. To quantitatively evaluate RNA hybrid duplex formation, expression vectors containing antisense dihydrofolate reductase (DHFR) cDNAs were transfected into KB and KB-1BT (a DHFR overexpressing variant) cells and transfectants expressing antisense transcripts of exon 1 through intron I (ex1-I) or exons 1 through 4 (ex1-4) were analyzed for hybrid duplex formation. Stable duplexes were detectable in KB-1BT but not in KB cells. Approximately 5-9% of antisense ex1-I RNA and 20-37% of antisense ex1-4 RNA were found in duplexes. The amount of each hybrid duplex RNA was found to be a linear function of intracellular single-stranded antisense RNA levels and a hybrid index, Hs:as, was devised to describe this relationship. Based upon the value of Hs:as for each antisense RNA:mRNA duplex, it is calculated that an approximate 2,800- and 600-fold excess of ex1-I and ex1-4 antisense RNA are respectively required for 50% of DHFR mRNA to be present in duplexes. Results support the hypothesis that intracellular sense:antisense RNA hybrid duplex formation is inefficient and dependent upon the levels, lengths and possibly the structures of the RNAs involved.
A Force-Directed Method for Large Crossing Angle Graph Drawing (2010)

Recent empirical research has indicated that human graph reading performance improves when crossing angles increase. However, crossing angle has not been used as an aesthetic criterion for graph drawing algorithms so far. In this paper, we introduce a force-directed method that aims to construct graph drawings with large crossing angles. Experiments indicate that our method significantly increases crossing angles. Surprisingly, the experimental results further demonstrate that the resulting drawings produced by our method have fewer edge crossings, a shorter total edge length and more uniform edge lengths, compared to classical spring algorithms.
Expression profile of innate immune receptors, NLRs and AIM2, in human colorectal cancer: correlation with cancer stages and inflammasome components (2015)

NLRs (nucleotide-binding domain leucine-rich repeat proteins or NOD-like receptors) are regulators of inflammation and immunity. A subgroup of NLRs and the innate immune receptor, AIM2 (absent-in-melanoma 2), can induce the assembly of a large caspase-1 activating complex called the inflammasome. Other NLRs regulate key signaling pathways such as NF-kB and MAPK. Since inflammation is a central component of colorectal cancer (CRC), this work was undertaken to analyze NLR and AIM2 expression in human CRC by combining bioinformatics analysis and experimental verification using clinical tissue samples. Additional experiments analyzed the association of (i) gene expression and cancer staging, and (ii) gene expression among inflammasome components.Ten public CRC datasets from the Oncomine® Platform were analyzed. Genes analyzed include NLRP1, NLRP3, NLRP6, NLRP12, NLRC3, NLRC4, NLRC5, NOD1, NOD2 and AIM2. Additionally, forty case-matched cancer samples and adjacent healthy control tissues isolated from a cohort of Chinese CRC patients were profiled.Three patterns of gene expression in CRC are shown. The expression of NLRC3, a checkpoint of inflammation, and the inflammasome components NLRP1, NLRP3, NLRC4 and AIM2 were reduced in CRC. NOD1 and NOD2 expression was increased in CRC, while NLRC5, NLRP6 and NLRP12 showed little difference compared to controls. Reduced expression of NLRC3 in CRC was verified in all available databases analyzed and confirmed with our patient cohort. Furthermore, the extent of NLRC3 and AIM2 gene reduction was correlated with cancer progression. This report reveals the potential value of NLR and AIM2 genes as biomarkers of CRC and cancer progression.
Differential T Cell Function and Fate in Lymph Node and Nonlymphoid Tissues (2002)

The functions and fate of antigen-experienced T cells isolated from lymph node or nonlymphoid tissues were analyzed in a system involving adoptive transfer of in vitro-activated T cells into mice. Activated T cells present in the lymph nodes could be stimulated by antigen to divide, produce effector cytokines, and migrate to peripheral tissues. By contrast, activated T cells that had migrated into nonlymphoid tissues (lung and airway) produced substantial effector cytokines upon antigen challenge, but were completely unable to divide or migrate back to the lymph nodes. Therefore, activated T cells can undergo clonal expansion in the lymph node, but are recruited and retained as nondividing cells in nonlymphoid tissues. These distinct regulatory events in lymph node and nonlymphoid tissues reveal simple key mechanisms for both inducing and limiting T cell immunity.
Active plate and wing research using EDAP elements (1992)

The deflection characteristics of structures using directionally attached piezoelectric (DAP) and enhanced DAP (EDAP) elements are explored. Tests demonstrate that piezoceramic elements, which are isotropic, exhibit orthotropic behavior when directionally attached using any of three methods: (i) partial attachment, (ii) transverse shear lag, and (iii) differential stiffness bonding. Test results demonstrate that directional enhancement through transverse stiffening can increase DAP element strain from 5 to 25%. Closed form expressions of DAP/EDAP strains based on classical laminated plate theory are presented. The models demonstrate that DAP/EDAP elements generate any in-plane strain (extensions and shear) or out-of-plane curvature (bending in either direction and twist) independent of other strains or curvatures. Test results show that fiberglass and aluminium DAP/EDAP beams produce torsional and bending deflections in excess of 30° m-1 with theory and experiment in close agreement. The deflections of DAP/EDAP and conventional piezoelectric active structures are compared. Tests show that DAP/EDAP elements can produce up to 16 times more twist than conventionally attached piezoceramic elements. Two wings were constructed with DAP and EDAP elements. EDAP elements were laminated into the skin of a graphite/epoxy supersonic wing that had a 9% thick diamond airfoil section and an aspect ratio of 3. DAP elements were also laminated to a torsion beam of a subsonic wing that had an NACA 0012 profile and an aspect ratio of 1.4. The supersonic wing demonstrated static twist deflections in excess of 2°. The subsonic wing demonstrated static pitch deflections of 9°. The lifting capability of the DAP/EDAP wings are compared to piezo-ailerons. The DAP/EDAP wings are shown to produce much larger changes in lift coefficient and greater deflection stability with increasing airspeed than the piezo-aileron configuration.
Band structure of acoustic waves in phononic lattices: Two-dimensional composites with large acoustic mismatch (2000)

The finite-difference time-domain method is applied to the calculation of dispersion relations of acoustic waves in two-dimensional (2D) phononic lattices, i.e., periodic solid-solid, solid-liquid, and solid-vacuum composites, for which the conventional plane-wave-expansion method fails or converges very slowly. Numerical examples are developed for 2D structures with polyethylene, mercury, and vacuum cylinders forming a square lattice in an aluminum matrix. The implication of the calculated dispersion relations for ultrasound transmission experiments is discussed.
1-Methylene sugars as C-glycoside precursors (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT1-Methylene sugars as C-glycoside precursorsT. V. RajanBabu and G. S. ReddyCite this: J. Org. Chem. 1986, 51, 26, 5458–5461Publication Date (Print):December 1, 1986Publication History Published online1 May 2002Published inissue 1 December 1986https://pubs.acs.org/doi/10.1021/jo00376a088https://doi.org/10.1021/jo00376a088research-articleACS PublicationsRequest reuse permissionsArticle Views1345Altmetric-Citations136LEARN 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
Characterization of VDAC1 as a plasma membrane NADH‐oxidoreductase (2004)

We have recently demonstrated that voltage dependent anion selective channel~1 (porin, isoform 1) can function as a transplasma membrane NADH:ferricyanide-reductase. However, both the specific redox characteristics and the mechanism of electron transport in this enzyme presently remain unclear. Here we demonstrate that the redox capability of porin 1 is specific for ferricyanide as this same enzyme cannot reduce DCIP or cytochrome c in vitro. Furthermore, NADH-dependent ferricyanide reduction associated with VDAC1 is not sensitive to the anion channel inhibitors DIDS and dextran sulfate. However, this activity can be inhibited by thiol chelators, suggesting that at least one of the two cysteine groups present in VDAC1 are critical for electron transfer. We propose a model on how electron transport may occur in VDAC1.
The IgA‐binding β antigen of the c protein complex of Group B streptococci: sequence determination of its gene and detection of two binding regions (1991)

The beta antigen of the lbc protein complex of Group B streptococci is a cell-surface receptor which binds the Fc region of human immunoglobulin A (IgA). Determination of the nucleotide sequence of the beta antigen gene shows that it encodes a preprotein having a molecular weight of 130,963 daltons and a polypeptide of 1164 amino acid residues that is typical of other Gram-positive cell-wall proteins. There is a long signal sequence of 37 amino acids at the N-terminus. Four of the five C-terminal amino acid residues are basic and are preceded by a hydrophobic stretch that appears to anchor the C-terminus in the cell membrane. To the N-terminal side of this hydrophobic stretch is a putative cell-wall-spanning region containing proline-rich repeated sequences. An unusual feature of these repeated sequences is a three-residue periodicity, whereby every first residue is a proline, the second residue is alternating positively or negatively charged, and the third residue is uncharged. The IgA-binding activity was approximately localized by expressing subfragments of the beta antigen as fusion proteins. Two distinct but adjacent DNA segments specified peptides that bound IgA, which indicates that the IgA-binding activity is located in two distinct regions of the protein.
Defects in mitochondrial localization and ATP synthesis in the mdx mouse model of Duchenne muscular dystrophy are not alleviated by PDE5 inhibition (2012)

Given the crucial roles for mitochondria in ATP energy supply, Ca(2+) handling and cell death, mitochondrial dysfunction has long been suspected to be an important pathogenic feature in Duchenne muscular dystrophy (DMD). Despite this foresight, mitochondrial function in dystrophin-deficient muscles has remained poorly defined and unknown in vivo. Here, we used the mdx mouse model of DMD and non-invasive spectroscopy to determine the impact of dystrophin-deficiency on skeletal muscle mitochondrial localization and oxidative phosphorylation function in vivo. Mdx mitochondria exhibited significant uncoupling of oxidative phosphorylation (reduced P/O) and a reduction in maximal ATP synthesis capacity that together decreased intramuscular ATP levels. Uncoupling was not driven by increased UCP3 or ANT1 expression. Dystrophin was required to maintain subsarcolemmal mitochondria (SSM) pool density, implicating it in the spatial control of mitochondrial localization. Given that nitric oxide-cGMP pathways regulate mitochondria and that sildenafil-mediated phosphodiesterase 5 inhibition ameliorates dystrophic pathology, we tested whether sildenafil's benefits result from decreased mitochondrial dysfunction in mdx mice. Unexpectedly, sildenafil treatment did not affect mitochondrial content or oxidative phosphorylation defects in mdx mice. Rather, PDE5 inhibition decreased resting levels of ATP, phosphocreatine and myoglobin, suggesting that sildenafil improves dystrophic pathology through other mechanisms. Overall, these data indicate that dystrophin-deficiency disrupts SSM localization, promotes mitochondrial inefficiency and restricts maximal mitochondrial ATP-generating capacity. Together these defects decrease intramuscular ATP and the ability of mdx muscle mitochondria to meet ATP demand. These findings further understanding of how mitochondrial bioenergetic dysfunction contributes to disease pathogenesis in dystrophin-deficient skeletal muscle in vivo.
Properties of homogeneous heat-labile enterotoxin from Escherichia coli (1980)

Recently, the heat-labile enterotoxin (LT) of Escherichia coli has been purified to homogeneity and partially characterized (Clements and Finkelstein, Infect. Immun. 24:760-769, 1979). This study extends our observations on the physicochemical properties of LT. The toxin has an isoelectric point of pH 8.0, as compared with choleragen and choleragenoid, which have isoelectric points of pH 6.75 and 7.75, respectively. Sedimentation equilibrium measurements established an approximate molecular weight for LT of 91,440. LT had an even more marked affinity than choleragen for agarose-containing matrixes in gel filtration. Of several mono- and disaccharides tested, only galactose and lactose were highly efficient in removing 125I-labeled LT from agarose-containing columns. LT dissociated into subunits (designated A and B) during gel filtration in the presence of 5 M guanidine. These subunits were immunologically distinct and possessed unique and shared antigenic determinants to the corresponding A and B subunits of choleragen. During gel filtration of LT at pH 6.5 and room temperature, a spontaneously occurring toxoid of LT, analogous to choleragenoid, was discovered and designated "coligenoid." This product contains only the B subunits of the toxin. A partial amino acid sequence of the B subunit of LT revealed a remarkable homology to the primary structure of cholera toxin B. Within the first 20 amino acids of the two chains, only 5 differ, and these differences may be attributable to single base substitutions.
Response features across the auditory midbrain reveal an organization consistent with a dual lemniscal pathway (2014)

The central auditory system has traditionally been divided into lemniscal and nonlemniscal pathways leading from the midbrain through the thalamus to the cortex. This view has served as an organizing principle for studying, modeling, and understanding the encoding of sound within the brain. However, there is evidence that the lemniscal pathway could be further divided into at least two subpathways, each potentially coding for sound in different ways. We investigated whether such an interpretation is supported by the spatial distribution of response features in the central nucleus of the inferior colliculus (ICC), the part of the auditory midbrain assigned to the lemniscal pathway. We recorded responses to pure tone stimuli in the ICC of ketamine-xylazine-anesthetized guinea pigs and used three-dimensional brain reconstruction techniques to map the location of the recording sites. Compared with neurons in caudal-and-medial regions within an isofrequency lamina of the ICC, neurons in rostral-and-lateral regions responded with shorter first-spike latencies with less spiking jitter, shorter durations of spiking responses, a higher proportion of spikes occurring near the onset of the stimulus, lower thresholds, and larger local field potentials with shorter latencies. Further analysis revealed two distinct clusters of response features located in either the caudal-and-medial or the rostral-and-lateral parts of the isofrequency laminae of the ICC. Thus we report substantial differences in coding properties in two regions of the ICC that are consistent with the hypothesis that the lemniscal pathway is made up of at least two distinct subpathways from the midbrain up to the cortex.
Vardenafil (2002)

Vardenafil hydrochloride is a potent and highly selective inhibitor of phosphodiesterase Type 5 that increases blood flow to the penis during sexual stimulation and helps restore the ability to achieve and sustain an erection in men with erectile dysfunction. Vardenafil was developed specifically to be an effective and safe oral medication for the treatment of erectile dysfunction, with potential advances over existing therapies. This review summarises key findings during the rapid and aggressive development of this compound, from in vitro assays to Phase III trials with both broad and special populations. Emphasis is placed on the presentation of data that demonstrates the clinical effectiveness and safety of this agent which is anticipated to be available in 2003.
Extended results of the Alzheimer's disease anti‐inflammatory prevention trial (2011)

These data suggest a revision of the original ADAPT hypothesis that NSAIDs reduce AD risk, as follows: NSAIDs have an adverse effect in later stages of AD pathogenesis, whereas asymptomatic individuals treated with conventional NSAIDs such as naproxen experience reduced AD incidence, but only after 2 to 3 years. Thus, treatment effects differ at various stages of disease. This hypothesis is consistent with data from both trials and epidemiological studies.
Depression of liver protein synthesis during surgery is prevented by growth hormone (1999)

This study was undertaken to elucidate the specific effects of growth hormone (GH) on liver protein metabolism in humans during surgery. Otherwise healthy patients scheduled for elective laparoscopic cholecystectomy were randomized into controls (n = 9) or pretreatment with 12 units of GH for 1 day (GH 1, n = 9) or daily for 5 days (GH 5, n = 10). The fractional synthesis rate of liver proteins, as assessed by flooding with [2H5]phenylalanine, was higher in the GH 5 group (22.0 +/- 6.9%/day, mean +/- SD, P < 0.05) than in the control (16.1 +/- 3.1%/day) and GH 1 (16.5 +/- 5.5%/day) groups. During surgery, the fraction of polyribosomes in the liver, as assessed by ribosome analysis, decreased in the control group by approximately 12% (P < 0.01) but did not decrease in the GH-treated groups. In addition, the concentrations of the essential amino acids and aspartate in the liver decreased in response to GH treatment. In conclusion, GH pretreatment decreases hepatic free amino acid concentrations and preserves liver protein synthesis during surgery.
Melanin-Concentrating Hormone Acutely Stimulates Feeding, But Chronic Administration Has No Effect on Body Weight (1997)

Melanin-concentrating hormone (MCH) has recently been proposed as both a central stimulator and an inhibitor of food intake. To clarify its role, we investigated the effects of MCH and the prepro-MCH-derived peptide neuropeptide E-I injected intracerebroventricularly (icv) in rats. MCH (0.15-15 micrograms) was injected icv at the beginning of the light phase. Food intake at 2 h showed a dose-dependent increase from 325 +/- 7% of the control value (1.5-microgram dose; P < 0.05) to 462 +/- 30% of the control value (15-microgram dose; P < 0.005). When 10 ng, 100 ng, and 5 micrograms MCH were injected icv at the beginning of the dark phase, only 5 micrograms stimulated feeding (166 +/- 16% of the control value; P < 0.05). At no dose did MCH inhibit feeding. Twice daily icv injections of MCH (5 micrograms) caused an average 197 +/- 9% increase in 2-h food intake for the first 5 days. Injections from days 6-8 did not stimulate feeding. Food intake and body weight at 24 h remained unchanged. Intracerebroventricular neuropeptide E-I had no effect on food intake alone and did not alter MCH-induced feeding. These studies show a dose-dependent stimulation of feeding by acute central administration of MCH. Tolerance is seen with chronic administration. These findings support a role for MCH in the immediate regulation of food intake, but not in body weight control.
Human cerebrospinal fluid central memory CD4+T cells: Evidence for trafficking through choroid plexus and meninges via P-selectin (2003)

Cerebrospinal fluid (CSF) from healthy individuals contains between 1,000 and 3,000 leukocytes per ml. Little is known about trafficking patterns of leukocytes between the systemic circulation and the noninflamed CNS. In the current study, we characterized the surface phenotype of CSF cells and defined the expression of selected adhesion molecules on vasculature in the choroid plexus, the subarachnoid space surrounding the cerebral cortex, and the cerebral parenchyma. Using multicolor flow cytometry, we found that CSF cells predominantly consisted of CD4+/CD45RA-/CD27+/CD69+-activated central memory T cells expressing high levels of CCR7 and L-selectin. CD3+ T cells were present in the choroid plexus stroma in autopsy CNS tissue sections from individuals who died without known neurological disorders. P- and E-selectin immunoreactivity was detected in large venules in the choroid plexus and subarachnoid space, but not in parenchymal microvessels. CD4+ T cells in the CSF expressed high levels of P-selectin glycoprotein ligand 1, and a subpopulation of circulating CD4+ T cells displayed P-selectin binding activity. Intercellular adhesion molecule 1, but not vascular cell adhesion molecule 1 or mucosal addressin cell adhesion molecule 1, was expressed in choroid plexus and subarachnoid space vessels. Based on these findings, we propose that T cells are recruited to the CSF through interactions between P-selectin/P-selectin ligands and intercellular adhesion molecule 1/lymphocyte function-associated antigen 1 in choroid plexus and subarachnoid space venules. These results support the overall hypothesis that activated memory T cells enter CSF directly from the systemic circulation and monitor the subarachnoid space, retaining the capacity to either initiate local immune reactions or return to secondary lymphoid organs.
Recommendations for the characterization of porous solids (Technical Report) (1994)

Abstract
Influence of cavity tuning on the transverse mode in vertical-cavity lasers (1995)

Data are presented showing the dependence of the transverse mode on the relative tuning of the cavity resonance to the gain peak in vertical-cavity surface-emitting lasers. Higher-order lasing modes are favored for the condition of a cavity resonant wavelength longer than that of the gain peak wavelength, while lower-order (single-lobed) radiation patterns are favored for the cavity resonance at a shorter wavelength than that of the gain peak.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>