gebhart/patrepeval huggingface dataset:
Surface-enhanced Raman scattering and the preparation of copper substrates for catalytic studies (1984)

Copper surfaces producing enhancement of the Raman scattering cross-section for adsorbed molecules comparable to the largest enhancements observed on silver have been prepared. These substrates are suitable for investigations of reactant intermediates in heterogeneous catalytic reactions, since they exhibit strong enhancement under atmospheric conditions. Roughening of the Cu surface involves etching with 2 mol dm–3 HNO3 or a combination of sandblasting and etching. The dye Nile Blue was adsorbed to test the Raman activity. The enhanced Raman spectrum of the molecule is analysed, and the dependence of the enhancement on etch time is investigated. For dye-laser excitation at 662 nm the observed surface enhancement is of the order of 103–104 for Nile Blue, which has an electronic absorption resonance, and of the order of 105–106 for p-nitrobenzoic acid, which is non-absorbing. Electron micrographs of the Cu surfaces show that with both roughening procedures maximum enhancement coincides with the creation of surface roughness features on the 10–100 nm scale, which corroborates present views on the size dependence of the electromagnetic enhancement contribution.
Cell-free DNA donor fraction analysis in pediatric and adult heart transplant patients by multiplexed allele-specific quantitative PCR: Validation of a rapid and highly sensitive clinical test for stratification of rejection probability (2020)

Lifelong noninvasive rejection monitoring in heart transplant patients is a critical clinical need historically poorly met in adults and unavailable for children and infants. Cell-free DNA (cfDNA) donor-specific fraction (DF), a direct marker of selective donor organ injury, is a promising analytical target. Methodological differences in sample processing and DF determination profoundly affect quality and sensitivity of cfDNA analyses, requiring specialized optimization for low cfDNA levels typical of transplant patients. Using next-generation sequencing, we previously correlated elevated DF with acute cellular and antibody-mediated rejection (ACR and AMR) in pediatric and adult heart transplant patients. However, next-generation sequencing is limited by cost, TAT, and sensitivity, leading us to clinically validate a rapid, highly sensitive, quantitative genotyping test, myTAIHEART®, addressing these limitations. To assure pre-analytical quality and consider interrelated cfDNA measures, plasma preparation was optimized and total cfDNA (TCF) concentration, DNA fragmentation, and DF quantification were validated in parallel for integration into myTAIHEART reporting. Analytical validations employed individual and reconstructed mixtures of human blood-derived genomic DNA (gDNA), cfDNA, and gDNA sheared to apoptotic length. Precision, linearity, and limits of blank/detection/quantification were established for TCF concentration, DNA fragmentation ratio, and DF determinations. For DF, multiplexed high-fidelity amplification followed by quantitative genotyping of 94 SNP targets was applied to 1168 samples to evaluate donor options in staged simulations, demonstrating DF call equivalency with/without donor genotype. Clinical validation studies using 158 matched endomyocardial biopsy-plasma pairs from 76 pediatric and adult heart transplant recipients selected a DF cutoff (0.32%) producing 100% NPV for ≥2R ACR. This supports the assay's conservative intended use of stratifying low versus increased probability of ≥2R ACR. myTAIHEART is clinically validated for heart transplant recipients ≥2 months old and ≥8 days post-transplant, expanding opportunity for noninvasive transplant rejection assessment to infants and children and to all recipients >1 week post-transplant.
Rapid Paper Chromatography or Carbohydrates and Related Compounds (1956)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRapid Paper Chromatography or Carbohydrates and Related CompoundsH. T. Gordon, Wayne. Thornburg, and L. N. WerumCite this: Anal. Chem. 1956, 28, 5, 849–855Publication Date (Print):May 1, 1956Publication History Published online1 May 2002Published inissue 1 May 1956https://doi.org/10.1021/ac60113a020RIGHTS & PERMISSIONSArticle Views241Altmetric-Citations343LEARN 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 InReddit PDF (941 KB) Get e-Alertsclose Get e-Alerts
Dendritic cells drive memory CD8 T-cell homeostasis via IL-15 transpresentation (2008)

Interleukin-15 (IL-15) is crucial for the development of naive and memory CD8 T cells and is delivered through a mechanism called transpresentation. Previous studies showed that memory CD8 T cells require IL-15 transpresentation by an as yet unknown cell of hematopoietic origin. We hypothesized that dendritic cells (DCs) transpresent IL-15 to CD8 T cells, and we examined this by developing a transgenic model that limits IL-15 transpresentation to DCs. In this study, IL-15 transpresentation by DCs had little effect on restoring naive CD8 T cells but contributed to the development of memory-phenotype CD8 T cells. The generation of virus-specific, memory CD8 T cells was partially supported by IL-15Ralpha(+) DCs through the preferential enhancement of a subset of KLRG-1(+)CD27(-) CD8 T cells. In contrast, these DCs were largely sufficient in driving normal homeostatic proliferation of established memory CD8 T cells, suggesting that memory CD8 T cells grow more dependent on IL-15 transpresentation by DCs. Overall, our study clearly supports a role for DCs in memory CD8 T-cell homeostasis but also provides evidence that other hematopoietic cells are involved in this function. The identification of DCs fulfilling this role will enable future studies to better focus on mechanisms regulating T-cell homeostasis.
Penetration and energy deposition of electrons in thick targets (1974)

The transport and energy deposition of fast electrons in multilayer targets are investigated. For a highly peaked distribution function of electrons impinging on a target, it is necessary to use a high-order diffusion theory to adequately represent the distribution function. To a first approximation the energy loss is neglected in any given layer. The average energy loss per layer is then calculated using the Bethe stopping power and knowledge of the electron multiple scattering. Once the beam penetrates a distance of about one-fifth the transport mean free path, it becomes possible to use the Bethe age diffusion equations provided that the atomic number ≥ 13 and the electron energies are below 1 MeV. A combination of the diffusion and high-order diffusion theory is also used to compute the backscattered current and energy. Limitations and regions of validity of the above theories are also discussed.
The CrIIL Reduction of [2Fe-2S] Ferredoxins and Site of Attachment of CrIII Using 1H NMR and Site-Directed Mutagenesis (2000)

The recently reported NMR solution structure of FeIIIFeIII parsley FdI has made possible 2D NOESY NMR studies to determine the point of attachment of CrIIIL in FeIIIFeIII...CrIIIL. The latter Cr-modified product was obtained by reduction of FeIIIFeIII parsley and spinach FdI forms with [Cr(15-aneN4) (H2O)2]2+ (15-aneN4 = 1,4,8,12-tetraazacyclopentadecane), referred to here as CrIIL, followed by air oxidation and chromatographic purification. From a comparison of NMR cross-peak intensities of native and Cr-modified proteins, two surface sites designated A and B, giving large paramagnetic CrIIIL broadening of a number of amino acid peaks, have been identified. The effects at site A (residues 19-22, 27, and 30) are greater than those at site B (residues 92-94 and 96), which is on the opposite side of the protein. From metal (ICP-AES) and electrospray ionization mass spectrometry (EIMS) analyses on the Cr-modified protein, attachment of a single CrIIIL only is confirmed for both parsley and spinach FdI and FdII proteins. Electrostatic interaction of the 3+ CrIIIL center covalently attached to one protein molecule (charge approximately -18) with a second (like) molecule provides an explanation for the involvement of two regions. Thus for 3-4 mM FeIIIFeIII...CrIIIL solutions used in NMR studies (CrIIIL attached at A), broadening effects due to electrostatic interactions at B on a second molecule are observed. Experiments with the Cys18Ala spinach FdI variant have confirmed that the previously suggested Cys-18 at site A is not the site of CrIIIL attachment. Line broadening at Val-22 of A gives the largest effect, and CrIIIL attachment at one or more adjacent (conserved) acidic residues in this region is indicated. The ability of CrIIL to bind in some (parsley and spinach) but not all cases (Anabaena variabilis) suggests that intramolecular H-bonding of acidic residues at A is relevant. The parsley and spinach FeIIFeIII...CrIIIL products undergo a second stage of reduction with the formation of FeIIFeII...CrIIIL. However, the spinach Glu92Ala (site B) variant undergoes only the first stage of reduction, and it appears that Glu-92 is required for the second stage of reduction to occur. A sample of CrIIIL-modified parsley FeIIIFeIII Fd is fully active as an electron carrier in the NADPH-cytochrome c reductase reaction catalyzed by ferredoxin-NADP+ reductase.
Caco‐2 cells as a model for intestinal lipoprotein synthesis and secretion (1995)

Caco-2 cells, an intestinal cell line derived from a human colorectal carcinoma that spontaneously differentiates under standard culture conditions, lends itself to the in vitro study of human gut in view of its efficient intestinal transport processes. Among its multiple biological functions are those related to the absorption, transport, and metabolism of lipids and lipoproteins. Despite their intestinal origin, confluent Caco-2 cell monolayers primarily express L-FABP for the uptake of apical dietary long chain fatty acids, incorporating them into triglycerides by the glycerol 3-phosphate pathway, and assembling very-low-density lipoprotein, high-density lipoprotein, and low-density lipoprotein. The monoacyl-glycerol pathway is inactive in Caco-2 cells. Furthermore, the secretion of newly synthesized triglyceride-rich lipoproteins is very restricted, despite abundant production of apolipoprotein (apo) B. The regulation of apoB synthesis and its mRNA editing at the enterocyte level has been intensively examined in Caco-2 cells. Luminal fatty acids, calcium ion, as well as vitamins and hormones are known to modulate the apoB-48/apoB-100 at the transcriptional and/or translational level. The regulation of 3-hydroxy-3-methylglutaryl-CoA reductase and acyl-CoA: (cholesterol acyltransferase), the key enzymes governing intracellular cholesterol handling, have also been extensively examined in Caco-2 cells. In many respects this cell line provides an excellent in vitro model for the investigation of intestinal lipoprotein metabolism; however, their limited secretion capacity remains a potential drawback to comparisons with the in vivo physiological state.
Effect of Kupffer cell phagocytosis of erythrocytes and erythrocyte ghosts on susceptibility to endotoxemia and bacteremia (1987)

The phagocytosis of erythrocytes by macrophages has previously been shown to depress macrophage function. In this study we compared the effect of the phagocytosis of erythrocytes and erythrocyte ghosts by Kupffer cells on the duration of the depression of complement receptor clearance function and host defense against endotoxemia and bacteremia. Phagocytosis of erythrocytes and erythrocyte ghosts was induced in rats by the injection of rat erythrocytes or erythrocyte ghosts coated with anti-rat erythrocyte immunoglobulin G (EIgG and GIgG, respectively). The hepatic uptake of EIgG and GIgG (17.4 X 10(8)/100 g) occurred during the first 30 min after injection. The digestion of phagocytized EIgG and GIgG, as assessed by electron microscopy, was complete at 24 and 3 h after injection, respectively. The depression of Kupffer cell complement receptor clearance function caused by EIgG and GIgG returned to normal by 6 h after injection of EIgG and by 3 h after injection of GIgG. Phagocytosis of EIgG depressed the survival rate after endotoxemia and bacteremia when endotoxin or bacteria were injected at 30 min after EIgG. The survival rate returned to normal when the endotoxin and bacteria were injected at 12 and 6 h after the EIgG, respectively. Phagocytosis of GIgG did not depress the survival rate after endotoxemia and bacteremia. Thus, compared with erythrocytes, erythrocyte ghosts are more rapidly digested after phagocytosis, depress complement receptor function for a shorter period of time, and cause less depression of host defense. These findings indicate that the contents of erythrocytes play an important role in the impairment of host defense caused by the phagocytosis of erythrocytes by Kupffer cells.
Migraine Pathophysiology and its Clinical Implications (2004)

The vascular hypothesis of migraine has now been superseded by a more integrated theory that involves both vascular and neuronal components. It has been demonstrated that the visual aura experienced by some migraineurs arises from cortical spreading depression, and that this neuronal event may also activate perivascular nerve afferents, leading to vasodilation and neurogenic inflammation of the meningeal blood vessels and, thus, throbbing pain. The involvement of the parasympathetic system supplying the meninges also causes increased vasodilation and pain. As an acute attack progresses, sensory neurones in the trigeminal nucleus caudalis become sensitized, resulting in the phenomenon of cutaneous allodynia. Triptans may act at several points during the progression of a migraine attack. However, the development of central sensitization impacts upon the effectiveness of triptan therapy.
Broad Clade 2 Cross-Reactive Immunity Induced by an Adjuvanted Clade 1 rH5N1 Pandemic Influenza Vaccine (2008)

ClinicalTrials.gov NCT00309634.
Bayesian transcriptome assembly (2014)

RNA sequencing allows for simultaneous transcript discovery and quantification, but reconstructing complete transcripts from such data remains difficult. Here, we introduce Bayesembler, a novel probabilistic method for transcriptome assembly built on a Bayesian model of the RNA sequencing process. Under this model, samples from the posterior distribution over transcripts and their abundance values are obtained using Gibbs sampling. By using the frequency at which transcripts are observed during sampling to select the final assembly, we demonstrate marked improvements in sensitivity and precision over state-of-the-art assemblers on both simulated and real data. Bayesembler is available at https://github.com/bioinformatics-centre/bayesembler .
Stability of molded polydimethylsiloxane microstructures (1997)

How stable are the features in elastomeric stamps —as used in microcontact printing (μCP) and micromolding in capillaries (MIMIC)—during their formation and subsequent application? Their stability is examined with respect to aspect ration and forces during handling. In the Figure, lines in the structure (gold on silicon), produced using an elastomeric stamp, can be seen to have merged into larger ensembles. magnified image
Alternative splicing of the telomerase catalytic subunit in human oocytes and embryos (1999)

The human telomerase catalytic subunit (hTCS) is a ribonucleoprotein which synthesizes telomere repeats on the ends of chromosomes. Telomerase activity is thought to be essential in maintaining normal telomere length in immortal (cancer) and germ cells. The objective of this study was to determine the gene expression of telomerase mRNA in human oocytes at different meiotic stages and in embryos. Normal and abnormal human oocytes, preimplantation embryos, and blastocysts were analysed for the presence and expression of the hTCS transcripts. Multiple telomerase mRNA products were identified by reverse transcription-polymerase chain reaction (RT-PCR) using primers within the reverse transcriptase domain. DNA sequencing of these amplicons suggest that there are alternative splicing variants which align to other telomerase reverse transcriptase (RT) consensus domains. Surprisingly, in unfertilized and immature gametes, as well as preimplantation embryos, hTCS expression revealed three different PCR product sizes, 457, 421 and 275 bp. The frequency of the 275 bp DNA product was 6.6% in oocytes (two out of 30) compared with 56.6% (17 out of 30) in poorly developing human preimplantation embryos (P < 0.005). The presence of alternately spliced mRNA variants in human preimplantation embryos may suggest a lack of telomerase activity and thus chromosomes associated with shortened telomeres.
Invasin production by Yersinia pestis is abolished by insertion of an IS200-like element within the inv gene (1996)

The two enteropathogens Yersinia pseudotuberculosis and Yersinia enterocolitica penetrate eukaryotic cells in vitro through invasin, a surface-exposed protein. In contrast, Yersinia pestis, the causative agent of plague, is unable to enter mammalian cell lines, although the inv gene is present on its chromosome. Although 99.3% identical to the inv gene of Y. pseudotuberculosis, the Y. pestis inv gene was disrupted in its central region by a 708-bp IS200-like element. Multiple copies of this insertion sequence element were found within the genome of the plague bacillus.
Butyrate Attenuates Lung Inflammation by Negatively Modulating Th9 Cells (2019)

Th9 cells orchestrate allergic lung inflammation by promoting recruitment and activation of eosinophils and mast cells, and by stimulating epithelial mucus production, which is known to be mainly dependent on IL-9. These cells share developmental pathways with induced regulatory T cells that may determine the generation of one over the other subset. In fact, the FOXP3 transcription factor has been shown to bind <i>il9</i> locus and repress IL-9 production. The microbiota-derived short-chain fatty acids (SCFAs) butyrate and propionate have been described as FOXP3 inducers and are known to have anti-inflammatory properties. While SCFAs attenuate lung inflammation by inducing regulatory T cells and suppressing Th2 responses, their effects on Th9 cells have not been addressed yet. Therefore, we hypothesized that SCFAs would have a protective role in lung inflammation by negatively modulating differentiation and function of Th9 cells. Our results demonstrated that butyrate is more effective than propionate in promoting FOXP3 expression and IL-9 repression. In addition, propionate was found to negatively impact <i>in vitro</i> differentiation of IL-13-expressing T cells. Butyrate treatment attenuated lung inflammation and mucus production in OVA-challenged mice, which presented lower frequency of lung-infiltrated Th9 cells and eosinophils. Both Th9 cell adoptive transfer and IL-9 treatment restored lung inflammation in butyrate-treated OVA-challenged mice, indicating that the anti-inflammatory effects of butyrate may rely on suppressing Th9-mediated immune responses.
CRYSTAL-INDUCED INFLAMMATION IN CANINE JOINTS (1966)

In an experimental model, the polymorphonuclear leukocyte was found to be necessary to the inflammation induced by crystals. This conclusion is based on (a) the invariable migration of polymorphonuclear leukocytes into the synovial fluid of canine joints injected with urate crystals, (b) the experimental suppression of the synovitis by the depletion of polymorphonuclear leukocytes in animals treated with vinblastine, (c) the dependence of the degree of suppression on the degree of leukocyte mobilization into the joint space, and (d) the restoration of the inflammatory response in a leukopenic animal by perfusion with normal blood.
Graft vs. host disease after liver transplantation: A new approach is needed (2007)

Graft-vs.-host disease (GVHD) is a rare, serious complication of orthotopic liver transplantation (OLT). We have treated 5 patients to date with GVHD after OLT. A total of 78 patients worldwide have been reported to have experienced this complication. The means by which GVHD after OLT has been managed is guided by experience with the more common GVHD that occurs after stem cell transplantation. However, despite the use of various treatment modalities, the mortality of GVHD after OLT remains high. This case series and review of the literature demonstrates that successful resolution of GVHD after OLT cannot be expected with the use of those modalities that have been tried to date. It is imperative that new treatments be applied to GVHD after OLT in order to improve the prognosis of patients with this diagnosis.
Childhood cardiovascular risk factors and carotid vascular changes in adulthood: the Bogalusa Heart Study. (2003)

Childhood measures of LDL-C level and BMI predict carotid IMT in young adults. The prevention implications of these findings remains to be explored.
The minimum peptide epitope from the influenza virus matrix protein. Extra and intracellular loading of HLA-A2 (1991)

Influenza virus matrix protein-derived peptides were synthesized based on the amino acid motifs for HLA-A2 bound self peptides. Among these peptides a nonamer (amino acids 58 through 66: G I L G F V F T L) was found to be 100 to 1000 times more effective than the commonly used peptide 57-68 (K G I L G F V F T L T V) in sensitizing HLA-A2+ target cells to lysis by influenza virus specific cytotoxic T lymphocytes. The sensitizing activity of the 12-mer 57-68 was not due to contamination with shorter and more active peptides. Intracellular expression of peptide 58-66 (mediated by a stable expression plasmid with DNA coding for this peptide) also sensitized HLA-A2+ cells to lysis. Peptide 58-66 stimulated human PBMC to generate CTL that recognized peptides 58-66 and 57-68 in association with HLA-A2.
Peroxidase-Mediated Oxidative Cross-Linking and Its Potential To Modify Mechanical Properties in Water-Soluble Polysaccharide Extracts and Cereal Grain Residues (2008)

Analysis of wheat bran and spent grain shows that concentrations of ferulate and diferulates offer considerable scope to modify the cross-linking of feruloylated polysaccharides and hence the mechanical properties of these residues. In solution ferulic acid (FA) can be readily polymerized by horseradish peroxidase, but when esterified to a polysaccharide, the profile of diferulates becomes restricted. This situation also exists in muro and suggests structural constraints may limit the availability of FA for cross-linking. At relatively low polysaccharide concentration, (approximately 3%), steric restrictions were apparent in gels prepared using isolated polysaccharides. Mechanical properties such as swelling also appear to be fixed at these relatively low polysaccharide concentrations. This limits the potential to modify mechanical properties in muro through oxidoreductase activity. To modify mechanical properties such treatments will need to focus on increasing the "flexibility" of the cell wall matrix and the accessibility of enzymes to the cell wall matrix.