gebhart/patrepeval huggingface dataset:
Peripheral Administration of Fetuin-A Attenuates Early Cerebral Ischemic Injury in Rats (2009)

Cerebral ischemia-elicited inflammatory responses are driven by inflammatory mediators produced both by central (e.g., neurons and microglia) and infiltrating peripheral immune cells (e.g., macrophage/monocyte), and contribute to the evolution of tissue injury. A ubiquitous molecule, spermine, is released from injured cells, and counter-regulates release of various proinflammatory cytokines. However, the spermine-mediated anti-inflammatory activities are dependent on the availability of fetuin-A, a liver-derived negative acute-phase protein. Using an animal model of focal cerebral ischemia (i.e., permanent middle cerebral artery occlusion, MCAo), we found that levels of fetuin-A in the ischemic brain tissue were elevated in a time-dependent manner, starting between 2 and 6 h, peaking around 24 to 48 h, and returning to baseline 72 h after MCAo. When administered peripherally, exogenous fetuin-A gained entry across the BBB into the ischemic brain tissue, and dose dependently reduced brain infarct volume at 24 h after MCAo. Meanwhile, fetuin-A effectively attenuated (i) ischemia-induced HMGB1 depletion from the ischemic core; (ii) activation of centrally (e.g., microglia) and peripherally derived immune cells (e.g., macrophage/monocytes); and (iii) TNF production in ischemic brain tissue. Taken together, these experimental data suggest that fetuin-A protects against early cerebral ischemic injury partly by attenuating the brain inflammatory response.
A second functional RNA domain in the 5′ UTR of the Tomato bushy stunt virus genome: Intra- and interdomain interactions mediate viral RNA replication (2003)

The 5' untranslated regions (UTRs) of (+)-strand RNA viruses play a variety of roles in the reproductive cycles of these infectious agents. Tomato bushy stunt virus (TBSV) belongs to this class of RNA virus and is the prototype member of the genus Tombusvirus. Previous studies have demonstrated that a T-shaped domain (TSD) forms in the 5' half of the TBSV 5' UTR and that it plays a central role in viral RNA replication. Here we have extended our structure-function analysis to the 3' half of the 5' UTR. Investigation of this region in the context of a model viral replicon (i.e., a TBSV-derived defective interfering [DI] RNA) revealed that this segment contains numerous functionally relevant structural features. In vitro solution structure probing along with comparative and computer-aided RNA secondary structure analyses predicted the presence of a simple stem loop (SL5) followed by a more complex downstream domain (DSD). Both structures were found to be essential for efficient DI RNA accumulation when tested in a plant protoplast system. For SL5, maintenance of the base of its stem was the principal feature required for robust in vivo accumulation. In the DSD, both helical and unpaired regions containing conserved sequences were necessary for efficient DI RNA accumulation. Additionally, optimal DI RNA accumulation required a TSD-DSD interaction mediated by a pseudoknot. Modifications that reduced accumulation did not appreciably affect DI RNA stability in vivo, indicating that the DSD and SL5 act to facilitate viral RNA replication.
Self-aggregation of kraft lignin in aqueous solutions. (2005)

Self-aggregation of kraft lignin in aqueous solution at various conditions was studied by light scattering. The tendency for kraft lignin to self-aggregate was found to increase either when the acidity, the ionic strength or the temperature was increased. From cryo-TEM analysis it was shown that the particle clusters formed exhibits fractal structures. By studying the kinetics of aggregation it was possible to distinguish between two different modes of aggregation from the fractal dimensions of the kraft lignin particles formed. The reaction limited cluster-colloid aggregation (RLCA) process creates denser particles whereas the diffusion limited cluster-colloid aggregation (DLCA) gives particles of looser shapes. Regarding the sensibility towards self-aggregation and precipitation by various monovalent electrolytes, the Hofmeister series for cations was found to be valid for kraft lignin. For anions, however, kraft lignin showed a reversed order of sensibility towards self-aggregation and precipitation compared with the Hofmeister series. The stability against self-aggregation was seen to increase dramatically when small amounts of bile acid salts were added to kraft lignin solutions. The outcome of these studies shows that in order to understand the solution behaviour of kraft lignin, sometimes kraft lignin should be treated as a macromolecule and sometimes as a colloid.
Human lymphocyte markers defined by antibodies derived from somatic cell hybrids. I. A hybridoma secreting antibody against a marker specific for human B lymphocytes. (1980)

A hybridoma has been isolated from the products of fusion of a myeloma cell line with spleen cells from mice immunized with a human B cell line. After cloning, the hybridoma secretes antibody with the following properties: (i) Human B-lymphoblastoid cell lines react with the antibody while T and null cell lines do not. (ii) The antibody reacts with the majority of leucocytes in the blood of patients with CLL, but with a minority of cells in the blood of patients with AML or ALL of the null or T type. (iii) The antibody reacts with 9-21% of mononuclear cells in normal peripheral blood. The reacting cells are not T cells and overlap extensively with cells identified as B cells by other markers. The antigen identified by this antibody appears to be distinct from known B cell markers, and is put forward as a new B cell marker with diagnostic potential.
Rituximab anti-B-cell therapy in systemic lupus erythematosus: pointing to the future (2005)

The findings reviewed point to a growing optimism for targeting B cells in the treatment of systemic lupus erythematosus; therefore double-blind studies comparing rituximab with existing immunosuppressive therapies are needed. Moreover, careful assessments of the effects of transient B-cell depletion on distinct autoimmune pathogenetic processes will enable optimization of therapeutic single or combined therapeutic schemes.
Genetic screening using the colour change of a PNA-DNA hybrid-binding cyanine dye (2002)

As the relationship between human genes and various malfunctions and diseases becomes revealed at an ever-increasing pace, the need arises for the development of rapid genetic screening methods for diagnostic purposes. Genetic diseases show great diversity. Some are caused by a few characteristic localised mutations, while others arise from a large number of variations. Hence, it is unlikely that a single, general diagnostic method that applies to all cases will ever exist. Instead, a combination of methods is frequently applied. Here we propose the use of a dramatic colour change that a cyanine dye, 3,3'-diethylthiadicarbocyanine, displays upon binding to DNA-PNA duplexes. This method could become an inexpensive, fast and simple genetic screening test by visual inspection, with no need for complicated equipment. Our results demonstrate that this diagnostic method may be sufficiently sensitive to discriminate between even a fully complementary and a single mutation DNA sequence.
Heterogeneous endolysins in Listeria monocytogenes bacteriophages: a new class of enzymes and evidence for conserved holin genes within the siphoviral lysis cassettes (1995)

Listeria monocytogenes bacteriophages A118, A500 and A511 are members of three distinct phage groups with characteristic host ranges. Their endolysin (ply) genes were cloned and expressed in Escherichia coli as demonstrated by the conferred lytic phenotype when colonies of recombinant cells were overlaid with a lawn of Listeria cells. The nucleotide sequences of the cloned DNA fragments were determined and the individual enzymes (PLY118, 30.8 kDa; PLY500, 33.4 kDa; PLY511, 36.5 kDa) were shown to have varying degrees of homology within their N-terminal or C-terminal domains. Transcriptional analysis revealed them to be 'late' genes with transcription beginning 15-20 min post-infection. The enzymes were overexpressed and partially purified and their individual specificities examined. When applied exogenously, the lysins induced rapid lysis of Listeria strains from all species but generally did not affect other bacteria. Using hydrolysis of purified listerial cell walls, PLY511 was characterized as an N-acetylmuramoyl-L-alanine amidase (EC 3.5.1.28) and shows homology in its N-terminal domain to other enzymes of this type. In contrast, PLY118 and PLY500 were shown to represent a new class of cell wall lytic enzymes which cleave between the L-alanine and D-glutamate residues of listerial peptidoglycan; these were designated as L-alanoyl-D-glutamate peptidases. These two enzymes share homology in the N-terminal domain which we propose determines hydrolytic specificity. Highly conserved holin (hol) gene sequences are present upstream of ply118 and ply500. They encode proteins of structural similarity to the product of phage lambda gene S, and are predicted to be membrane proteins which form pores to allow access of the lysins to their peptidoglycan substrates. This arrangement of conserved holin genes with downstream lysin genes among the siphoviral lysis cassettes explains why the cytoplasmic endolysins alone are not lethal, since they require a specific transport function across the cell membrane.
Amino acid sequence of beta-galactosidase. IV. Sequence of an alpha-complementing cyanogen bromide peptide, residues 3 to 92. (1975)

Intracistronic alpha-complementation between a cyanogen bromide digest of beta-galactosidase and an extract of the lac Zminus operator-proximal deletion mutant M15 was used to monitor the purification of a cyanogen bromide peptide (CB2) responsible for the complementation. Key steps in the purification were ion exchange chromatography on carboxymethylcellulose and sulfopropyl-Sephadex in the presence of urea, and Sephadex gel filtration. CB2 contains residues 3 to 92 of beta-galactosidase. Its sequence is: Ile-Thr-Asp-Ser-Leu-Ala-Val-Val-Leu-Gln-Arg-Arg-Asp-Trp-Glu-Asn-Pro-Gly-Val-Thr-Gln-Leu-Asn-Arg-Leu-Ala-Ala-His-Pro-Pro-Phe-Ala-Ser-Trp-Arg-Asn-Ser-Glu-Glu-Ala-Arg-Thr-Asp-Arg-Pro-Ser-Gln-Gln-Leu-Arg-Ser-Leu-Asn-Gly-Glu-Trp-Arg-Phe-Ala-Trp-Phe-Pro-Ala-Pro-Glu-Ala-Val-Pro-Glu-Ser-Trp-Leu-Glu-Cys-Asp-Leu-Pro-Glu-Ala-Asp-Thr-Val-Val-Val-Pro-Ser-Asn-Trp-Gln-Met. Thus no more than 1/13 of the beta-galactosidase polypeptide chain, starting 2 residues from the NH2 terminus, is necessary for alpha-complementation with M15 as alpha-acceptor.
Cloning, expression, and localization of a rat brain high-affinity glycine transporter. (1992)

A cDNA clone encoding a glycine transporter has been isolated from rat brain by a combined PCR and plaque-hybridization strategy. mRNA synthesized from this clone (designated GLYT1) directs the expression of sodium- and chloride-dependent, high-affinity uptake of [3H]glycine by Xenopus oocytes. [3H]Glycine transport mediated by clone GLYT1 is blocked by sarcosine but is not blocked by methyl-aminoisobutyric acid or L-alanine, a substrate specificity similar to that described for a previously identified glycine-uptake system called system Gly. In situ hybridization reveals that GLYT1 is prominently expressed in the cervical spinal cord and brainstem, two regions of the central nervous system where glycine is a putative neurotransmitter. GLYT1 is also strongly expressed in the cerebellum and olfactory bulb and is expressed at lower levels in other brain regions. The open reading frame of the GLYT1 cDNA predicts a protein containing 633 amino acids with a molecular mass of approximately 70 kDA. The primary structure and hydropathicity profile of GLYT1 protein reveal that this protein is a member of the sodium- and chloride-dependent superfamily of transporters that utilize neurotransmitters and related substances as substrates.
Experimental and numerical analysis of flow behavior in the FASTRAC liquid composite manufacturing process (2004)

Abstract The success of resin infusion during liquid composite processing depends on several factors; including the complete impregnation of the dry performs, the processing conditions, and the tooling used during processing. New process developments based on the Fast Remotely Actuated Channels (FASTRAC) process aid the infusion with the creation of preferential resin flow paths using a non‐contact tooling. Experiments to understand and study the infusion behavior with the presence of the FASTRAC non‐contacting tooling have been performed, and compared with vacuum‐assisted processes without such tooling. Experimental studies indicate that the infusion time with FASTRAC channel configurations is significantly less despite the additional volume regions to be infused during processing. The use of a non‐contacting interchangeable tool, the improved infusion behavior, and the significant reduction in the infusion time provide significant advantages for processing advanced composite systems, including the potential to use high viscosity resin systems, and process automation. The process simulation models of the experimental configurations based on the thin shell model configurations have been compared with experimental observations. Studies indicate that the process simulation models and approaches employed clearly emulate the infusion behavior seen when the channels are present, validating the modeling strategies employed. Similar simulation approaches will thus be effective to study and understand various FASTRAC tooling configurations while processing complex composite structures. Polym. Compos. 25:384–396, 2004. © 2004 Society of Plastics Engineers.
A novel recessive Nefl mutation causes a severe, early‐onset axonal neuropathy (2009)

This is the first demonstration of a recessive NEFL mutation, which appears to cause a simple loss of function, resulting in a severe, early-onset axonal neuropathy with unique features. These results confirm that neurofilaments are the main determinant of axonal caliber and conduction velocity, and demonstrate for the first time that neurofilaments are required for the maintenance of myelinated peripheral nervous system axons.
Improved phase vocoder time-scale modification of audio (1999)

The phase vocoder is a well established tool for time scaling and pitch shifting speech and audio signals via modification of their short-time Fourier transforms (STFTs). In contrast to time-domain time-scaling and pitch-shifting techniques, the phase vocoder is generally considered to yield high quality results, especially for large modification factors and/or polyphonic signals. However, the phase vocoder is also known for introducing a characteristic perceptual artifact, often described as "phasiness", "reverberation", or "loss of presence". This paper examines the problem of phasiness in the context of time-scale modification and provides new insights into its causes. Two extensions to the standard phase vocoder algorithm are introduced, and the resulting sound quality is shown to be significantly improved. Moreover, the modified phase vocoder is shown to provide a factor-of-two decrease in computational cost.
Validated caloric expenditure estimation using a single body-worn sensor (2009)

In 2007, approximately 30% of US adults were obese, with related health care costs exceeding 100 billion dollars. Clearly, the obesity epidemic represents a growing societal concern. One challenge in weight control is the difficulty of tracking food calories consumed and calories expended by activity. This paper presents a system for automatic monitoring of calories expended using a single body-worn accelerometer. Our system uses activity inference combined with signal analysis to estimate calories expended in real-time using regression formulas developed by the American College of Sports Medicine. To validate our system, we have collected data from 51 subjects in a laboratory setting using a treadmill and a more natural field test. Actual caloric expenditure was determined using the medical "gold standard" measurement, of oxygen consumption. We are able to achieve 89% accuracy with lab data and 79% with field data -- both high enough to be useful in practice.
Microporous Metal–Organic Frameworks with High Gas Sorption and Separation Capacity (2007)

Abstract The design, synthesis, and structural characterization of two microporous metal–organic framework structures, [M(bdc)(ted) 0.5 ]·2 DMF·0.2 H 2 O (M = Zn ( 1 ), Cu ( 2 ); H 2 bdc = 1,4‐benzenedicarboxylic acid; ted = triethylenediamine; DMF: N , N ‐dimethylformamide) is reported. The pore characteristics and gas sorption properties of these compounds are investigated at cryogenic temperatures, room temperature, and higher temperatures by experimentally measuring argon, hydrogen, and selected hydrocarbon adsorption/desorption isotherms. These studies show that both compounds are highly porous with a pore volume of 0.65 ( 1 ) and 0.52 cm 3 g – 1 ( 2 ). The amount of the hydrogen uptake, 2.1 wt % ( 1 ) and 1.8 wt % ( 2 ) at 77 K (1 atm; 1 atm = 101 325 Pa), places them among the group of metal–organic frameworks (MOFs) having the highest H 2 sorption capacity. [Zn(bdc)(ted) 0.5 ]·2 DMF·0.2 H 2 O adsorbs a very large amount of hydrocarbons, including methanol, ethanol, dimethylether (DME), n ‐hexane, cyclohexane, and benzene, giving the highest sorption values among all metal–organic based porous materials reported to date. In addition, these materials hold great promise for gas separation.
ICAM-2 and a Peptide from Its Binding Domain Are Efficient Activators of Leukocyte Adhesion and Integrin Affinity (1999)

Cell adhesion mediated by the CD11/CD18 integrins and their ligands, the ICAMs, is required for many leukocyte functions. In resting cells the integrins are nonadhesive, but when activated they become adhesive for their ligands. Previous findings have shown that a peptide derived from the first Ig domain of ICAM-2 (P1) binds to LFA-1 (CD11a/CD18) and Mac-1 (CD11b/CD18) and activates leukocyte aggregation. Because its mechanism of action has remained poorly understood, we have now studied the peptide-induced ligand binding in detail. Here we show that P1 was able to induce CD11/CD18-dependent adhesion of human T lymphocytes to immobilized, purified ICAM-1, -2, and -3. The optimal peptide concentration was 150 micrograms/ml, whereas concentrations higher than 400 micrograms/ml did not have any stimulatory effect. The increase in adhesion was detectable within 10 min of treatment with the peptide; it was dependent on energy, divalent cations, temperature, and an intact cytoskeleton but was unaffected by protein kinase C and protein tyrosine kinase inhibitors. Peptide treatment resulted in strong stimulation of the binding of soluble, recombinant ICAMs to T lymphocytes, showing that the integrin affinity toward its ligands was increased. Importantly, soluble ICAM-2Fc was also able to induce T lymphocyte adhesion to purified ICAM-1, -2, and -3, and it was a more potent stimulatory molecule than ICAM-1Fc or ICAM-3Fc.
Poly(oligonucleotide) (2014)

Here we report the preparation of poly(oligonucleotide) brush polymers and amphiphilic brush copolymers from nucleic acid monomers via graft-through polymerization. We describe the polymerization of PNA-norbornyl monomers to yield poly-PNA (poly(peptide nucleic acid)) via ring-opening metathesis polymerization (ROMP) with the initiator, (IMesH2)(C5H5N)2(Cl)2RuCHPh.1 In addition, we present the preparation of poly-PNA nanoparticles from amphiphilic block copolymers and describe their hybridization to a complementary single-stranded DNA (ssDNA) oligonucleotide.
Efficient generation of single and entangled photons on a silicon photonic integrated chip (2011)

We present a protocol for generating on-demand, indistinguishable single photons on a silicon photonic integrated chip. The source is a time-multiplexed spontaneous parametric down-conversion element that allows optimization of single-photon versus multiphoton emission while realizing high output rate and indistinguishability. We minimize both the scaling of active elements and the scaling of active element loss with multiplexing. We then discuss detection strategies and data processing to further optimize the procedure. We simulate an improvement in single-photon-generation efficiency over previous time-multiplexing protocols, assuming existing fabrication capabilities. We then apply this system to generate heralded Bell states. The generation efficiency of both nonclassical states could be increased substantially with improved fabrication procedures.
Buxus alkaloids. XIII. Synthetic approach to the 9(10.fwdarw. 19)abeopragnane system (1967)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBuxus alkaloids. XIII. Synthetic approach to the 9(10.fwdarw. 19)abeopragnane systemS. Morris. Kupchan, Elie. Abushanab, Kolla T. Shamasundar, and Arnold W. ByCite this: J. Am. Chem. Soc. 1967, 89, 24, 6327–6332Publication Date (Print):November 1, 1967Publication History Published online1 May 2002Published inissue 1 November 1967https://pubs.acs.org/doi/10.1021/ja01000a060https://doi.org/10.1021/ja01000a060research-articleACS PublicationsRequest reuse permissionsArticle Views175Altmetric-Citations9LEARN 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
Competitive ArC−H and ArC−X (X = Cl, Br) Activation in Halobenzenes at Cationic Titanium Centers (2006)

The titanium methyl cation [Cp*((tBu3P=N)TiCH3]+ [B(C6F5)4]- reacts rapidly with H2 to give the analogous cationic hydride [Cp*((tBu3P=N)TiH(THF)n]+ [B(C6F5)4]- (n = 0, 1), which can be trapped and isolated as its THF adduct 1 x THF (n = 1). When generated in the presence of chloro or bromobenzene, 1 undergoes C-X activation or ortho-C-H activation, depending on the amount of dihydrogen present in the reaction medium. At approximately 4 atm of H2, C-X activation is preferred, giving the halocations [Cp*((tBu3P= N)TiX]+ [B(C6F5)4]- (2X) and C6H6/biphenyl mixtures. At lower pressures of H2 (>1 atm), the beta-halophenyl cations [Cp*((tBu3P=N)Ti(2-X-C6H4)]+ [B(C6F5)4]- (3X) are the products isolated. In the absence of H2, these compounds are quite thermally stable, but undergo beta-halogen elimination upon moderate heating, to give 2X (approximately 20%) and compounds 4X which are the result of reaction between 2X and benzyne via addition of the benzyne C-C triple bond across the Ti-N bond of the phosphinimide ligand. Thus, three separate bond activation processes are operative in this system: direct C-X activation, ortho-C-H activation, and indirect C-X activation via beta-halogen elimination. Mechanistic studies on all three processes have been done and support a radical pathway for direct C-X cleavage, sigma-bond metathesis of the ortho-C-H bond of eta(1)-coordinated C6H5X, and beta-halogen elimination from base-free compound 3X.