gebhart/patrepeval huggingface dataset:
Variable Number of Tandem Repeat (VNTR) Markers for Human Gene Mapping (1987)

A large collection of good genetic markers is needed to map the genes that cause human genetic diseases. Although nearly 400 polymorphic DNA markers for human chromosomes have been described, the majority have only two alleles and are thus uninformative for analysis of genetic linkage in many families. A few known marker systems, however, detect loci that respond to restriction enzyme cleavage by producing a fragment that can have many different lengths. This polymorphism is due to variation in the number of tandem repeats of a short DNA sequence. Because most individuals will be heterozygous at such loci, these markers will provide linkage information in almost all families. Ten oligomeric sequences derived from the tandem repeat regions of the myoglobin gene, the zeta-globin pseudogene, the insulin gene, and the X-gene region of hepatitis B virus, were used to develop a series of single-copy probes. These probes revealed new, highly polymorphic genetic loci whose allele sizes reflected variation in the number of tandem repeats.
Analysis of the Increase and Decreas, e Algorithms for Congestion Avoidance in Computer Networks (2009)

Abstract. Congestion avoidance mechanisms allow a network to operate in the optimal region of low delay and high throughput, thereby, preventing the network from becoming congested. This is different from the traditional congestion control mechanisms that allow the network to recover from the congested state of high delay and low throughput. Both con-gestion avoidance and congestion control mechanisms are basi-cally resource management problems. They can be formulated as system control problems in which the system senses its state and feeds this back to its users who adjust their controls. The key component of any congestion avoidance scheme is the algorithm (or control function) used by the users to in-crease or decrease their load (window or rate). We abstractly characterize a wide class of such increase/decrease algorithms and compare them using several different performance metrics. They key metrics are efficiency, fairness, convergence time, and size of oscillations. It is shown that a simple additive increase and multiplicative decrease algorithm satisfies the sufficient conditions for con-vergence to an efficient and fair state regardless of the starting state of the network. This is the algorithm finally chosen for implementation in the congestion avoidance scheme recom-
PURIFICATION AND CHARACTERIZATION OF POLYSACCHARIDES EXTRACTED FROM Tremella fuciformis AND Auricularia auricula (2012)

For decades, many studies reported and suggested the therapeutic uses of polysaccharides extracted from various sources, especially from wild mushrooms. Tremella fuciformis and Auricularia auricula are edible fungi commonly abundant in Thailand, and the major component found both fungi is polysaccharides. T. fuciformis and A. auricula have long been studied for its medicinal purposes such as anti-oxidant, anti-tumor property, anticoagulant activity, hypoglycemic activity, memory improvement, etc. Even though some studies reported potential pharmacological activities of the polysaccharides extracted from T. fuciformis and A. auricular. The chemical composition and efficiency of extraction processes of polysaccharides in T. fuciformis and A. auricula were not completely clear. We, therefore, purposed this study to purify and characterize the polysaccharides isolated from T. fuciformis and A. auricula. The polysaccharides purification process for T. fuciformis and A. auricula were performed by using the method suggested by Yoon et al. (2003) with some modification until purified polysaccharides obtained. Proteins contamination was determined by BCA protein assay and SDS-PAGE gel. Nucleic acids contamination was measured by using UV– Vis spectrophotometer at 260 nm wavelength. Using this method, our results showed that purified polysaccharides from both fungi were white in color indicating no pigments contamination. The yields of purified polysaccharides from A. auricula and T. fuciformis were around 0.84% and 2.0% (w/w) with around 80% and 91% polysaccharides purity (expressed as glucose/xylose and mannose/xylose combined), respectively. The proteins and nucleic acids contaminants were small amounts, less than 0.25% and around 0.8% in A. auricular, and less than 0.25% and around 3.0% in T. fuciformis. In summary, we successfully obtained the purified polysaccharides from T. fuciformis and A. auricula with high purity and low in pigments, proteins and nucleic acids contaminants.
Pyrolysis of volatile aromatic hydrocarbons and n-heptane over calcium oxide and quartz (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPyrolysis of volatile aromatic hydrocarbons and n-heptane over calcium oxide and quartzDaniel L. Ellig, Chiu K. Lai, David W. Mead, John P. Longwell, and William A. PetersCite this: Ind. Eng. Chem. Process Des. Dev. 1985, 24, 4, 1080–1087Publication Date (Print):October 1, 1985Publication History Published online1 May 2002Published inissue 1 October 1985https://pubs.acs.org/doi/10.1021/i200031a031https://doi.org/10.1021/i200031a031research-articleACS PublicationsRequest reuse permissionsArticle Views254Altmetric-Citations52LEARN 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 options Get e-Alerts
Expression of the antiviral protein Mx in peripheral blood mononuclear cells of pregnant and bred, non-pregnant ewes (2001)

Interferon-tau (IFN tau) acts locally on the endometrium to suppress estrogen and oxytocin receptor expression and block luteolysis in ruminants. Systemic administration of conceptus homogenates or recombinant ovine IFN tau does not block luteolysis or enhance pregnancy rates in sheep or cattle, respectively. However, IFN tau up-regulates expression of the antiviral protein Mx throughout the entire uterine wall during early pregnancy. These studies determined if conceptus-derived IFN tau also up-regulates Mx expression in components of the circulating immune system that migrate through the endometrial wall. In experiment one, peripheral blood mononuclear cells (PBMC) were isolated from ewes at D26 post-artificial insemination (AI) and Mx mRNA levels examined by Northern and slot-blot hybridization. Pregnancy resulted in a two-fold increase in Mx mRNA levels compared to bred, non-pregnant ewes at D26. In experiment two, PBMC were isolated from ewes at AI, and every three days from D9 to D30. Results showed a four-fold increase in Mx mRNA levels in PBMC from pregnant versus bred, non-pregnant ewes at D15. Increased Mx mRNA, which remained elevated through D30, was accompanied by increased levels of Mx protein. These results show that pregnancy recognition signaling rapidly induces Mx gene expression in PBMC, and are the first to suggest that IFN tau activates gene expression in components of the circulating immune system.
Preparation, Characterization, and Application of Au-Shell/Polystyrene Beads and Au-Shell/Magnetic Beads (2001)

Multifunctional core–shell particles composed of magnetic particles covered with a gold nanoshell can be induced to align into conducting lines upon application of a magnetic field (see Figure). The formation of Au clusters and “streaky” gold nanoparticles on the surface of the PS beads is demonstrated and the preparation, characterization, and applications of magnetic and polystyrene beads featuring a gold shell are addressed.
Catalytic Partial Oxidation of Cyclohexane by Bimetallic Ag/Pd Nanoparticles on Magnesium Oxide (2017)

The liquid-phase oxidation of cyclohexane to cyclohexanol and cyclohexanone was investigated by synthesizing and testing an array of heterogeneous catalysts comprising: monometallic Ag/MgO, monometallic Pd/MgO and a set of bimetallic AgPd/MgO catalysts. Interestingly, Ag/MgO was capable of a conversion comparable to current industrial routes of approximately 5 %, and with a high selectivity (up to 60 %) to cyclohexanol, thus making Ag/MgO an attractive system for the synthesis of intermediates for the manufacture of nylon fibres. Furthermore, following the doping of Ag nanoparticles with Pd, the conversion increased up to 10 % whilst simultaneously preserving a high selectivity to the alcohol. Scanning transmission electron microscopy and energy dispersive spectroscopy of the catalysts showed a systematic particle-size-composition variation with the smaller Ag-Pd nanoparticles being statistically richer in Pd. Analysis of the reaction mixture by electron paramagnetic resonance (EPR) spectroscopy coupled with the spin-trapping technique showed the presence of large amounts of alkoxy radicals, thus providing insights for a possible reaction mechanism.
Characterization and prediction of protein nucleolar localization sequences (2010)

Although the nucleolar localization of proteins is often believed to be mediated primarily by non-specific retention to core nucleolar components, many examples of short nucleolar targeting sequences have been reported in recent years. In this article, 46 human nucleolar localization sequences (NoLSs) were collated from the literature and subjected to statistical analysis. Of the residues in these NoLSs 48% are basic, whereas 99% of the residues are predicted to be solvent-accessible with 42% in α-helix and 57% in coil. The sequence and predicted protein secondary structure of the 46 NoLSs were used to train an artificial neural network to identify NoLSs. At a true positive rate of 54%, the predictor's overall false positive rate (FPR) is estimated to be 1.52%, which can be broken down to FPRs of 0.26% for randomly chosen cytoplasmic sequences, 0.80% for randomly chosen nucleoplasmic sequences and 12% for nuclear localization signals. The predictor was used to predict NoLSs in the complete human proteome and 10 of the highest scoring previously unknown NoLSs were experimentally confirmed. NoLSs are a prevalent type of targeting motif that is distinct from nuclear localization signals and that can be computationally predicted.
The monogenic signal (2001)

This paper introduces a two-dimensional (2-D) generalization of the analytic signal. This novel approach is based on the Riesz transform, which is used instead of the Hilbert transform. The combination of a 2-D signal with the Riesz transformed one yields a sophisticated 2-D analytic signal: the monogenic signal. The approach is derived analytically from irrotational and solenoidal vector fields. Based on local amplitude and local phase, an appropriate local signal representation that preserves the split of identity, i.e., the invariance-equivariance property of signal decomposition, is presented. This is one of the central properties of the one-dimensional (1-D) analytic signal that decomposes a signal into structural and energetic information. We show that further properties of the analytic signal concerning symmetry, energy, allpass transfer function, and orthogonality are also preserved, and we compare this with the behavior of other approaches for a 2-D analytic signal. As a central topic of this paper, a geometric phase interpretation that is based on the relation between the 1-D analytic signal and the 2-D monogenic signal established by the Radon (1986) transform is introduced. Possible applications of this relationship are sketched, and references to other applications of the monogenic signal are given.
Lung Injury Secondary to Chemotactic Factor-Induced Leukocyte Activation (1983)

Intravascular complement activation in rats following thermal injury or vascular infusion of cobra venom factor results in acute lung injury as determined morphologically and measured by increases in lung vascular permeability. The acute lung injury is associated with the early appearance of C5-derived chemotactic activity in the circulation coincident with the development of neutropenia. The lung injury is closely linked to availability of complement and neutrophils and can be prevented by systemic treatment of animals with a combination of superoxide dismutase and catalase, specific inhibitors of toxic oxygen metabolites. These data suggest that intravascular complement activation leads to activation of neutrophils and their intrapulmonary capillary sequestration, and subsequent acute lung injury, which is associated with production and release of oxygen-derived free radicals by C5a-activated blood neutrophils.
Catalytic Properties of Human Manganese Superoxide Dismutase (1996)

The depletion of superoxide catalyzed by human manganese superoxide dismutase (MnSOD) was observed spectrophotometrically by measuring the absorbance of superoxide at 250-280 nm following pulse radiolysis and by stopped-flow spectrophotometry. Catalysis showed an initial burst of activity lasting approximately 1 ms followed by the rapid emergence of a greatly inhibited catalysis of zero-order rate. These catalytic properties of human MnSOD are qualitatively similar to those reported for MnSOD from Thermus thermophilus (Bull, C., Niederhoffer, E. C., Yoshida, T., and Fee, J. A.(1991) J. Am. Chem. Soc. 113, 4069-4076). However, there are significant quantitative differences; the emergence of the inhibited form is approximately 30-fold more rapid for human MnSOD. The turnover number for human MnSOD at pH 9.4 and 20 degrees C was kcat = 4 x 10(4) s-1 and kcat/Km = 8 x 10(8) M-1 s-1, determined by a simulated fit of the model of Bull et al. (1991) to the pulse radiolysis data. We also report that the maximum of the visible absorption spectrum of human MnSOD (epsilon480 = 525 M-1 cm-1) showed a strong dependence on pH that could be described by an ionization of pKa 9.4 +/- 0.1 with a maximum at low pH.
Targeting of Hematologic Malignancies with PTC299, A Novel Potent Inhibitor of Dihydroorotate Dehydrogenase with Favorable Pharmaceutical Properties (2018)

PTC299 was identified as an inhibitor of VEGFA mRNA translation in a phenotypic screen and evaluated in the clinic for treatment of solid tumors. To guide precision cancer treatment, we performed extensive biological characterization of the activity of PTC299 and demonstrated that inhibition of VEGF production and cell proliferation by PTC299 is linked to a decrease in uridine nucleotides by targeting dihydroorotate dehydrogenase (DHODH), a rate-limiting enzyme for <i>de novo</i> pyrimidine nucleotide synthesis. Unlike previously reported DHODH inhibitors that were identified using <i>in vitro</i> enzyme assays, PTC299 is a more potent inhibitor of DHODH in isolated mitochondria suggesting that mitochondrial membrane lipid engagement in the DHODH conformation <i>in situ</i> is required for its optimal activity. PTC299 has broad and potent activity against hematologic cancer cells in preclinical models, reflecting a reduced pyrimidine nucleotide salvage pathway in leukemia cells. Archived serum samples from patients treated with PTC299 demonstrated increased levels of dihydroorotate, the substrate of DHODH, indicating target engagement in patients. PTC299 has advantages over previously reported DHODH inhibitors, including greater potency, good oral bioavailability, and lack of off-target kinase inhibition and myelosuppression, and thus may be useful for the targeted treatment of hematologic malignancies.
The proteins of ISGF-3, the interferon alpha-induced transcriptional activator, define a gene family involved in signal transduction. (1992)

ISGF-3 is a multiprotein transcription factor that is very quickly activated in the cell cytoplasm only after attachment of interferon alpha to the cell surface. To understand the specific cytoplasmic activation of proteins that move to the nucleus and direct increased transcription of specific genes, we have purified and now report completion of the cloning of cDNA encoding the four proteins of ISGF-3. With all of the sequences available, it is clear that three of these proteins are encoded by members of a previously unrecognized gene family. We suggest that proteins encoded by this gene family serve the function of interpreting the fact that a cell surface receptor has bound its ligand so that specific signal transduction to the nucleus can occur.
Chemokine receptor targeting efficiently directs antigens to MHC class I pathways and elicits antigen-specific CD8+ T-cell responses (2006)

Chemokines are key controllers of cell trafficking and are involved in numerous pathologic and inflammatory conditions. However, the fate of a chemokine ligand, once it is endocytosed with its receptor, remains obscure. Here, using chemokine-tumor antigen fusion constructs, we demonstrate for the first time that chemokines are internalized to early/late endosomal and lysosomal compartments through a clathrin-dependent process and subsequently delivered to the cytosol for proteasomal processing, facilitating efficient cross-presentation to the TAP-1-dependent MHC class I processing pathway. These data not only elucidate the intracellular fate of chemokine ligands upon receptor uptake, but also demonstrate the superior carrier potency of chemokines for delivering self-antigens to both class I and II processing pathways to induce CD8(+) and CD4(+) T-cell responses.
Halogenated indoles eradicate bacterial persister cells and biofilms (2016)

The emergence of antibiotic resistance has necessitated new therapeutic approaches to combat recalcitrant bacterial infections. Persister cells, often found in biofilms, are metabolically dormant, and thus, are highly tolerant to all traditional antibiotics and represent a major drug resistance mechanism. In the present study, 36 diverse indole derivatives were investigated with the aim of identifying novel compounds that inhibit persisters and biofilm formation by Gram-negative Escherichia coli and Gram-positive Staphylococcus aureus. 5-Iodoindole and other halogenated indoles, 4-fluoroindole, 7-chloroindole, and 7-bromoindole, eradicated persister formation by E. coli and S. aureus, and 5-iodoindole most potently inhibited biofilm formation by the two bacteria. Unlike other antibiotics, 5-iodoindole did not induce persister cell formation, and 5-iodoindole inhibited the production of the immune-evasive carotenoid staphyloxanthin in S. aureus; hence, 5-iodoindole diminished the production of virulence factors in this strain. These results demonstrate halogenated indoles are potentially useful for controlling bacterial antibiotic resistance.
The molecular biology of arteriviruses. (1998)

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.
Neurocytotoxicity: pharmacological implications (1991)

Summary— Recent data suggest that brain damage in ischemia, hypoglycemia, and several other brain diseases is caused by excitotoxic mechanisms which are triggered by presynaptic release of glutamate and related excitatory amino acids, and which involve an abnormal postsynaptic influx of calcium into cells containing a high density of glutamate receptors. This contention is supported by results demonstrating reduction of infarct size in focal ischemia due to middle cerebral artery (MCA) occlusion, and amelioration of neuronal necrosis in hypoglycemic coma, by antagonist which block the NMDA type of glutamate receptor. These results underscore the pathogenetic role of calcium influx into energy‐compromised cells since the NMDA receptor‐linked ion channel has a high conductance to calcium. The issue has been clouded by the inability of NMDA antagonists to ameliorate brain damage due to cardiac arrest, or to forebrain ischemia in rats and gerbils. In these conditions, however, an AMPA receptor blocker (NBQX) has been found efficacious. These results demonstrate that the pathophysiology of ischemic lesions is different in the cardiac arrest type of ischemia and in lesions due to MCA occlusion, and demand an explanation of the differences in therapeutic response. Tentatively, the cardiac arrest type of ischemia is so dense that multiple calcium conductances are activated in the energy‐deprived tissue, explaining why any drug which acts on only one of them (such as an NMDA antagonist) cannot prevent cellular calcium overload. Futher‐more the ultimate brain damage, which is often conspicuously delayed, may be secondary to upregulation of synaptic efficacy, causing increased calcium cycling and calcium‐related damage. In this situation, an AMPA receptor blocker may be efficacious because it blocks “fast” excitation and Na+ influx, an “upstream” event which causes “downstream” calcium influx via multiple pathways. In the perifocal (“penumbra”) zone of a stroke lesion, the situation is different since depolarisation is initially moderate and/or intermittent. Furthermore, since ATP is still produced (albeit at a reduced rate) the problem is one of a disturbed pump/leak relationship. Then, blockade of a major calcium‐carrying channel by NMDA receptor blockers, or of the trigger to depolarisation by an AMPA receptor antagonist, may improve the pump/leak relationship and carry cells in the penumbra over a critical period.
Risk of aspirin-associated major upper-gastrointestinal bleeding with enteric-coated or buffered product (1996)

Use of low doses of enteric-coated or buffered aspirin carries a three-fold increase in the risk of major UGIB. The assumption that these formulations are less harmful than plain aspirin may be mistaken.
Oligomeric and Fibrillar Species of Amyloid-β Peptides Differentially Affect Neuronal Viability (2002)

Genetic evidence predicts a causative role for amyloid-beta (A beta) in Alzheimer's disease. Recent debate has focused on whether fibrils (amyloid) or soluble oligomers of A beta are the active species that contribute to neurodegeneration and dementia. We developed two aggregation protocols for the consistent production of stable oligomeric or fibrillar preparations of A beta-(1-42). Here we report that oligomers inhibit neuronal viability 10-fold more than fibrils and approximately 40-fold more than unaggregated peptide, with oligomeric A beta-(1-42)-induced inhibition significant at 10 nm. Under A beta-(1-42) oligomer- and fibril-forming conditions, A beta-(1-40) remains predominantly as unassembled monomer and had significantly less effect on neuronal viability than preparations of A beta-(1-42). We applied the aggregation protocols developed for wild type A beta-(1-42) to A beta-(1-42) with the Dutch (E22Q) or Arctic (E22G) mutations. Oligomeric preparations of the mutations exhibited extensive protofibril and fibril formation, respectively, but were not consistently different from wild type A beta-(1-42) in terms of inhibition of neuronal viability. However, fibrillar preparations of the mutants appeared larger and induced significantly more inhibition of neuronal viability than wild type A beta-(1-42) fibril preparations. These data demonstrate that protocols developed to produce oligomeric and fibrillar A beta-(1-42) are useful in distinguishing the structural and functional differences between A beta-(1-42) and A beta-(1-40) and genetic mutations of A beta-(1-42).