gebhart/patrepeval huggingface dataset:
The Subviral RNA Database: a toolbox for viroids, the hepatitis delta virus and satellite RNAs research (2006)

With its design, the Subviral RNA Database could be considered as a fundamental building block for the study of these related RNAs. It is freely available via a web browser at the URL: http://subviral.med.uottawa.ca.
Immunological characterization of papain-induced fragments of Clostridium botulinum type A neurotoxin and interaction of the fragments with brain synaptosomes (1989)

After treatment of Clostridium botulinum type A neurotoxin with papain, three fragments (Mrs, 101,000, 45,000, and 43,000) were purified by hydrophobic and ion-exchange chromatography with a high-performance liquid chromatographic system. Immunoblotting analyses with monoclonal antibodies showed that the 101,000-dalton fragment consisted of the light chain and a part of the heavy chain (H-1 fragment) linked together by a disulfide bond, and the other two fragments were correlated to the remaining portion of the heavy chain (H-2 fragment). The 45,000- and 43,000-dalton fragments effectively competed for binding of the 125I-labeled neurotoxin to synaptosomes, while no inhibition was observed with the 101,000-dalton fragment. The results indicate that the H-2 fragment interacts with the binding site on the neural membrane. The binding of the neurotoxin was impaired by treatment of synaptosomes with neuraminidase. Incorporation of gangliosides into neuraminidase-treated synaptosomes resulted in the restoration of binding. The results suggest that gangliosides are one of the components of the toxin-binding site.
Tuftsin (an Ig-associated tetrapeptide) triggers the immunogenic function of macrophages: implications for activation of programmed cells. (1978)

The immunoglobulin heavy-chain-associated tetrapeptide, tuftsin (Thr-Lys-Pro-Arg), known for its phagocytosis-stimulating activity, was found to augment the antigen-specific, macrophage-dependent education of T lymphocytes. The investigation of stereospecific characteristics of the tetrapeptide, by use of structural analogs with different modifications, revealed strict structural requirements for eliciting the immunogenic activity of macrophages. It was found that the most important moiety for its activity is the dipeptide Pro-Arg. This finding is of interest in view of the appearance of this particular dipeptide in other bioregulatory peptides, including many of the peptide hormones. The significance of the appearance of a common structure in such molecules, which may act through specific receptors on different target cells, is discussed.
Inflammatory response in Parkinson’s disease (Review) (2014)

Parkinson's disease (PD) is one of the most common age‑related neurodegenerative diseases, which results from a number of environmental and inherited factors. PD is characterized by the slow progressive degeneration of dopaminergic (DA) neurons in the substantia nigra. The nigrostriatal DA neurons are particularly vulnerable to inflammatory attack. Neuroinflammation is an important contributor to the pathogenesis of age‑related neurodegenerative disorders, such as PD, and as such anti‑inflammatory agents are becoming a novel therapeutic focus. This review will discuss the current knowledge regarding inflammation and review the roles of intracellular inflammatory signaling pathways, which are specific inflammatory mediators in PD. Finally, possible therapeutic strategies are proposed, which may downregulate inflammatory processes and inhibit the progression of PD.
Automatically Constructing a Corpus of Sentential Paraphrases. (2005)

An obstacle to research in automatic paraphrase identification and genera-tion is the lack of large-scale, publicly-available labeled corpora of sentential paraphrases. This paper describes the creation of the recently-released Micro-soft Research Paraphrase Corpus, which contains 5801 sentence pairs, each hand-labeled with a binary judg-ment as to whether the pair constitutes a paraphrase. The corpus was created using heuristic extraction techniques in conjunction with an SVM-based classi-fier to select likely sentence-level para-phrases from a large corpus of topic-clustered news data. These pairs were then submitted to human judges, who confirmed that 67 % were in fact se-mantically equivalent. In addition to describing the corpus itself, we explore a number of issues that arose in defin-ing guidelines for the human raters.
Requirements for Internet Hosts - Application and Support (1989)

This RFC is an official specification for the Internet community. It incorporates by reference, amends, corrects, and supplements the primary protocol standards documents relating to hosts. Distribution of this document is unlimited. Summary This RFC is one of a pair that defines and discusses the requirements for Internet host software. This RFC covers the application and support protocols; its companion RFC-1122 covers the communication protocol layers: link layer, IP layer, and transport layer.
A modelling study of once-bred heifer beef production (1991)

A case farm study of a once-bred heifer system on hill country using a spreadsheet simulation model was undertaken. Results of the feed budget and financial data of the once-bred system were compared with bull beef, 18 month heifer ftishing and traditional breeding cow policies. lheonce-bmdheifersystemgeneratedagrossmarginof$48.26/s.u. comparedwith$42.50/s.u.foratraditionalbreedingcowbreeding system, $31.7O/s.u for the 20 month heifer finishing and $52.8O/s.u. for a bull beef system. The once-bred heifer system produced 3 14 kg carcasslha. the breeding system cow 197 kg carcass/ha, the 20 month heifer system 354 kg carcass/ha and the bull beef system 433 kg carcass/ ha. The major factor affecting the profiibility of the once-bred heifer system was schedule price. ‘Ihe best match of animal requirements and pasture growth for the ume-bred heifer system was shown to occur for an October calving. This study suggests that sheep and beef farmers with traditional beef cattle policies could increase productivity by adopting a once-bred heifer beef production system.
Isolation of cDNAs for perilipins A and B: sequence and expression of lipid droplet-associated proteins of adipocytes. (1993)

The major cAMP-dependent protein kinase (A-kinase) substrate in adipocytes is perilipin, a protein found exclusively at the surface of the lipid storage droplets. Using anti-perilipin serum, we have isolated two related classes of full-length coding cDNAs, designated perilipin A and B, from a rat adipocyte cDNA expression library. The two cDNAs derive from two mRNA species that arise by differential splicing. The mRNAs are predicted to encode perilipins A and B, proteins of 517 aa (56,870 Da) and 422 aa (46,420 Da), respectively, which share a common 406-aa N-terminal sequence. The predicted perilipin A contains peptides present in proteolytic digests of the purified 62-kDa form of perilipin from rat adipocytes, as well as the requisite consensus A-kinase phosphorylation sites. Like perilipin A, the B form is expressed in adipocytes and is associated with lipid storage droplets. Modeling of predicted secondary structures fails to reveal an underlying basis for the tenacious association of perilipins with lipid droplets. These proteins exhibit a significant sequence relationship (approximately 65% similarity through 105 aa) with only one other known protein, the adipocyte differentiation-related protein (ADRP). Like the perilipins, ADRP appears to be adipocyte-specific, which suggests that they interact in a related intracellular pathway. The molecular probes for perilipins A and B described here will permit detailed analyses of their functional role(s) in lipid metabolism.
Proteolytic release of CD44 intracellular domain and its role in the CD44 signaling pathway (2001)

CD44 is a widely distributed cell surface adhesion molecule and is implicated in diverse biological processes. However, the nature of intracellular signaling triggered by CD44 remains to be elucidated. Here, we show that CD44 undergoes sequential proteolytic cleavage in the ectodomain and intracellular domain, resulting in the release of a CD44 intracellular domain (ICD) fragment. Consequently, CD44ICD acts as a signal transduction molecule, where it translocates to the nucleus and activates transcription mediated through the 12-O-tetradecanoylphorbol 13-acetate-responsive element, which is found in numerous genes involved in diverse cellular processes. Expression of an uncleavable CD44 mutant as well as metalloprotease inhibitor treatment blocks CD44-mediated transcriptional activation. In search of the underlying mechanism, we have found that CD44ICD potentiates transactivation mediated by the transcriptional coactivator CBP/p300. Furthermore, we show that cells expressing CD44ICD produce high levels of CD44 messenger RNA, suggesting that the CD44 gene is one of the potential targets for transcriptional activation by CD44ICD. These observations establish a novel CD44 signaling pathway and shed new light on the functional link between proteolytic processing of an adhesion molecule at the cell surface and transcriptional activation in the nucleus.
Pharmacogenetics of Antidepressants (2011)

Up to 60% of depressed patients do not respond completely to antidepressants (ADs) and up to 30% do not respond at all. Genetic factors contribute for about 50% of the AD response. During the recent years the possible influence of a set of candidate genes as genetic predictors of AD response efficacy was investigated by us and others. They include the cytochrome P450 superfamily, the P-glycoprotein (ABCB1), the tryptophan hydroxylase, the catechol-O-methyltransferase, the monoamine oxidase A, the serotonin transporter (5-HTTLPR), the norepinephrine transporter, the dopamine transporter, variants in the 5-hydroxytryptamine receptors (5-HT1A, 5-HT2A, 5-HT3A, 5-HT3B, and 5-HT6), adrenoreceptor beta-1 and alpha-2, the dopamine receptors (D2), the G protein beta 3 subunit, the corticotropin releasing hormone receptors (CRHR1 and CRHR2), the glucocorticoid receptors, the c-AMP response-element binding, and the brain-derived neurotrophic factor. Marginal associations were reported for angiotensin I converting enzyme, circadian locomotor output cycles kaput protein, glutamatergic system, nitric oxide synthase, and interleukin 1-beta gene. In conclusion, gene variants seem to influence human behavior, liability to disorders and treatment response. Nonetheless, gene × environment interactions have been hypothesized to modulate several of these effects.
Interaction and functional collaboration of p300/CBP and bHLH proteins in muscle and B-cell differentiation. (1996)

Differentiation of skeletal muscle cells and B lymphocytes is regulated by basic helix-loop-helix (bHLH) proteins. Both differentiation programs are inhibited by the adenovirus E1A oncoprotein. Analysis of E1A mutants has implicated two of its cellular-binding proteins, p300 and CBP, in controlling certain aspects of differentiation. We find that p300 can cooperate with tissue-specific bHLH proteins in activating target genes and requires only the bHLH domain of such proteins to stimulate E box-directed transcription. Importantly, the ability of bHLH proteins to activate transcription correlates with the presence of p300/CBP in E box-dependent DNA-binding complexes, because both phenomena require at least two adjacent E-box motifs. Microinjection of p300/CBP antibodies into myoblasts blocks terminal differentiation, cell fusion, and transcriptional activity of myogenic bHLH proteins. These results suggest that the function of p300/CBP is essential for the execution of key aspects of cellular differentiation.
Impurity Effect in the Ionization Dilatation of Vitreous Silica (1968)

The normal effect of ionizing radiation is to cause a contraction. Vitreous silica which colors in the visible (presumably because of its aluminum content) shows a very rapid radiation-induced expansion which soon saturates. Thus, depending on the impurity composition, the vitreous silica may show an initial decreased contraction or an initial expansion followed by subsequent contraction. Data are given for the optical absorption and the dilatation, for x-ray, gamma-ray, and electron irradiations. The dilatation was measured by interferometric and photoelastic methods, and for the latter, the method was further developed. The expansion was found to have a different distribution along the range of electrons than the contraction. Spontaneous annealing was found for the expansion, but not for the contraction. The thermal annealing of the dilatation and optical absorption were studied. In the coloring vitreous silica, the expansion annealed at a lower temperature than the contraction. The expansion and the contraction appear to be quite independent. The expansion is explained as caused by breaking Al–O links in the structure, the contraction by a compaction of the Si–O structure. Variation in absorption behavior associated with OH content is attributed largely to the kinds of centers formed in the vicinity of impurities rather than the number of radiation-induced atomic configurations which can form centers.
The maturation of mucus-secreting gastric epithelial progenitors into digestive-enzyme secreting zymogenic cells requires Mist1 (2006)

Continuous regeneration of digestive enzyme (zymogen)-secreting chief cells is a normal aspect of stomach function that is disrupted in precancerous lesions (e.g. metaplasias, chronic atrophy). The cellular and genetic pathways that underlie zymogenic cell (ZC) differentiation are poorly understood. Here, we describe a gene expression analysis of laser capture microdissection purified gastric cell populations that identified the bHLH transcription factor Mist1 as a potential ZC regulatory factor. Our molecular and ultrastructural analysis of proliferation, migration and differentiation of the gastric unit in Mist1(-/-) and control mice supports a model whereby wild-type ZC progenitors arise as neck cells in the proliferative (isthmal) zone of the gastric unit and become transitional cells (TCs) with molecular and ultrastructural characteristics of both enzyme-secreting ZCs and mucus-secreting neck cells as they migrate to the neck-base zone interface. Thereafter, they rapidly differentiate into mature ZCs as they enter the base. By contrast, Mist1(-/-) neck cells differentiate normally, but ZCs in the mature, basal portion of the gastric unit uniformly exhibit multiple apical cytoplasmic structural abnormalities. This defect in terminal ZC differentiation is also associated with markedly increased abundance of TCs, especially in late-stage TCs that predominantly have features of immature ZCs. Thus, we present an in vivo system for analysis of ZC differentiation, present molecular evidence that ZCs differentiate from neck cell progenitors and identify Mist1 as the first gene with a role in this clinically important process.
Transfer RNA Cleavages by Onconase Reveal Unusual Cleavage Sites (2006)

Onconase, a protein from amphibian eggs and a homologue of pancreatic ribonuclease (RNase) superfamily, is cytotoxic, exhibits antitumor and antiviral activity, and is in phase III clinical trials. It has been shown to predominantly target cellular tRNA on its entry into mammalian cells (Saxena, S. K., Sirdeshmukh, R., Ardelt, W., Mikulski, S. M., Shogen, K., and Youle, R. J. (2002) J. Biol. Chem. 277, 15142-15146). Cleavage site mapping using natural tRNA substrates, in vitro, revealed predominant cleavage sites at UG and GG residues. Cleavages at UG or the less intense cleavages at CG sites are consistent with the known base specificity of onconase. However, predominance of cleavages at selected G-G bonds is unusual for a homologue of pancreatic RNases. Interestingly, in at least three of the four tRNA substrates studied, the predominant cleavages mapped in the triplet UGG located in the context of the variable loop or the D-arm of the tRNA. The cleavage specificity of onconase observed by us thus indicates another special feature of this enzyme, which may be relevant to its cellular actions.
A New Approach for Vision-based Rear Vehicle Tracking (2007)

A thorough research of dynamic target tracking problem in vision system on intelligent vehicle is conducted. A new approach to track of the rear part of a vehicle by a backward-looking video camera is put forward. Considered that the target's relative speed is slow and the shape changes little, the vehicle fast tracking is obtained by locating the edge of target in tracking window. The tracking accuracy is improved by computing the target comparability feature to conduct self-evaluation of the location reliability, and the location deviation is emendated by template match algorithm. The stably tracking of vehicle target in complex background is achieved, and the tracking accuracy is higher than 90 percent. When the tracking window is shifting, the tracking can be resumed automatically by this algorithm.
Two Signaling Mechanisms for Activation of αMβ2 Avidity in Polymorphonuclear Neutrophils (1998)

Circulating polymorphonuclear neutrophils (PMN) are quiescent, nonadherent cells that rapidly activate at sites of inflammation, where they develop the capacity to perform a repertoire of functions that are essential for host defense. Induction of integrin-mediated adhesion, which requires an increase in integrin avidity, is critical for the development of these effector functions. Although a variety of stimuli can activate integrins in PMN, the signaling cascades involved are unclear. Phosphatidylinositol (PI) 3-kinase has been implicated in integrin activation in a variety of cells, including PMN. In this work, we have examined activation of the PMN integrin alphaM beta2, assessing both adhesion and generation of the epitope recognized by the activation-specific antibody CBRM1/5. We have found that PI 3-kinase has a role in activation of alphaM beta2 by immune complexes, but we have found no role for it in alphaM beta2 activation by ligands for trimeric G protein-coupled receptors, including formylmethionylleucylphenylalanine (fMLP), interleukin-8, and C5a. Cytochalasin D inhibition suggests a role for the actin cytoskeleton in immune complex activation of alphaM beta2, but cytochalasin has no effect on fMLP-induced activation. Similarly, immune complex activation of the Rac/Cdc42-dependent serine/threonine kinase Pak1 is blocked by PI 3-kinase inhibitors, but fMLP-induced activation is not. These results demonstrate that two signaling pathways exist in PMN for activation of alphaM beta2. One, induced by FcgammaR ligation, is PI 3-kinase-dependent and requires the actin cytoskeleton. The second, initiated by G protein-linked receptors, is PI 3-kinase-independent and cytochalasin-insensitive. Pak1 may be in a final common pathway leading to activation of alphaM beta2.
Phylogenetic Relationship of Chlamydia pneumoniae to Chlamydia psittaci and Chlamydia trachomatis as Determined by Analysis of 16S Ribosomal DNA Sequences (1993)

The 16S ribosomal DNA sequence of Chlamydia pneumoniae was determined and compared with the corresponding gene sequences of Chlamydia psittaci and Chlamydia trachomatis. C. pneumoniae has been reported to exhibit little chromosomal DNA homology with the other chlamydial species, and its phylogenetic relationships within the genus Chlamydia have not been described. A polymerase chain reaction was employed to determine the 16S rRNA gene sequence of C. pneumoniae. Ten primers from the C. psittaci sequences were used to amplify a C. pneumoniae template in overlapping segments of the gene. Sequence data for 1,554 bases indicated that the levels of homology of C. pneumoniae with C. psittaci and C. trachomatis were 96.19 and 94.07%, respectively. These data support the results of previous biochemical and developmental studies indicating that C. pneumoniae is more closely related to C. psittaci than to C. trachomatis.
A Simple Relaxation Scheme for Polar Codes (2018)

In this paper, a simple relaxation scheme to reduce the encoding and decoding complexity of polar codes is introduced. Unlike the conventional relaxation schemes, the proposed technique relies on selecting relevant encoding/decoding nodes based on initialized relaxation attribute values and their extension to the remainder of the encoder and decoder stages. We show that the proposed relaxation scheme provides comparable BLER performance to the conventional polar codes by numerical simulations, while having significant complexity reduction.
Phase 1b randomized, double-blind study of namilumab, an anti-granulocyte macrophage colony-stimulating factor monoclonal antibody, in mild-to-moderate rheumatoid arthritis (2017)

ClinicalTrials.gov, NCT01317797 . Registered 18 February 2011.
Mechanism of cross-resistance between vincristine and daunorubicin in Ehrlich ascites tumor cells. (1978)

Abstract An investigation was undertaken of the mechanism of a previously reported cross-resistance between vincristine (VCR) and daunorubicin (DNR) in Ehrlich ascites tumor cells. No significant difference was demonstrated for the time course of [3H]VCR uptake in cells resistant to VCR (EHR 2/VCR+) and in cells resistant to DNR (EHR 2/DNR+), whereas wild-type cells accumulated nearly 6-fold more drug at steady state. The energy dependence of [3H]VCR and of DNR transport was investigated by the metabolic inhibitors sodium azide and iodoacetic acid. These studies revealed that uptake of [3H]VCR and of DNR was depressed in both resistant sublines by an energy-dependent process that mostly requires energy from glycolysis. If glucose was omitted from the medium together with addition of sodium azide, the uptake of [3H]VCR and of DNR in EHR 2/VCR+ reached a level nearly equal to that of wild-type cells. If glycolysis was restored by addition of glucose to the resistant cells loaded with drug in this way, a pronounced extrusion of [3H]VCR and of DNR was induced. In a similar experiment with wild-type cells, a slight but significant extrusion of [3H]VCR could be induced. The studies showed that, for nearly unidirectional influx, the cells must be incubated in the medium without glucose but with sodium azide. In this medium the influx of [3H]VCR and of DNR was significantly higher in wild-type cells than in cells from the resistant sublines. The flux of DNR was not competitively inhibited by VCR either in wild-type cells or in resistant cells. The data indicate that the mechanism of cross-resistance between VCR and DNR in Ehrlich ascites tumor cells is a result of at least two different mechanisms: (a) an energy-dependent drug extrusion common to VCR and DNR; and (b) unspecific changes in the membrane, which reduce the influx of both compounds.
Relationship between differing volumes of bone marrow aspirates and their cellular composition. (1990)

We compared the cellular composition of the first 1.0 ml volume bone marrow aspirate with that of an aliquot from the total bone marrow harvest at the end of the procedure in 17 healthy bone marrow donors. Each sample was assayed for its content of red blood cells, nucleated cells, CD2+, CD4+, CD8+, CD19+, HLA-DR+, CD56+, CD13+, CD33+, CD34+ and KiM8+ cells and CFU-GM. On the basis of data obtained, we estimated that the first 1.0 ml samples had 8.0 +/- 5.2% (SD) and the transplant samples 20.8 +/- 8.5% contamination with nucleated blood cells. The calculation revealed that both types of bone marrow samples had 100% volume contamination with peripheral blood, i.e. that bone marrow cells were aspirated within blood fluid volume. Nucleated cell concentration was 3-fold, and CFU-GM concentration 10-fold lower in the transplant than in the first-puncture 1.0 ml bone marrow samples. Various marker-positive cells appeared in transplant samples in concentrations that depended on their abundance in the first-puncture 1.0 ml and blood samples. Taken together, our data suggest that bone marrow harvesting would be substantially improved if individual aspirates were small in volume and taken from bone puncture sites as distant as possible.