gebhart/patrepeval huggingface dataset:
Resilience of Malic Acid Natural Deep Eutectic Solvent Nanostructure to Solidification and Hydration (2017)

Little is presently known about the unique nanostructure of deep eutectic solvents (DES). The order of the liquid-solid phase transition is contended and whether DES-water mixtures are merely aqueous solutions, or have properties dominated by the eutectic pair, is unclear. Here, we unambiguously show the structure of choline chloride-malic acid (malicine) as a liquid, and also in solid and hydrated forms, using neutron total scattering on D/H isotope-substituted samples, and quasi-elastic neutron scattering (QENS). Data were refined using empirical potential structure refinement. We show evidence for a stoichiometric complex ion cluster in the disordered liquid, with strong choline-chloride bonding and a hydrogen bond donor (HBD) contribution. The 1:1 eutectic stoichiometry makes these ionic domains more well-defined, with less HBD clustering than seen previously for reline. There is minimal structural difference for the solidified material, demonstrating that this DES solidification is a glass transition rather than a first order phase change. QENS data support this by showing a gradual change in solvent dynamics rather than a step change. The DES structure is mostly retained upon hydration, with water acting both as a secondary smaller HBD at closer range to choline than malic acid, and forming transient wormlike aggregates. This new understanding of DES structure will aid understanding of the properties of these novel green solvents on the molecular length scale in chemical processes, as well as giving an insight into the apparent role of natural DESs in plant physiology.
Bombesin may stimulate proliferation of human pancreatic cancer cells through an autocrine pathway (1996)

Bombesin is trophic to normal pancreas and acinar cell adenocarcinoma, but its effects on ductal cell tumors are undetermined. The autocrine growth effects of bombesin on well-differentiated (HPAF, CD11) and poorly differentiated (CD18, PANC-1) human ductal pancreatic cancer cell lines were investigated. Receptor binding of labeled bombesin was measured in a whole-cell microplate assay. Bombesin production was measured by radioimmunoassay. Proliferative responses were quantified using the MTT assay. Messenger RNA for bombesin and its receptor were identified by primer extension analysis. A single class of high-affinity binding sites was detected on HPAF and CD18 cells. Similar affinities and high receptor densities were found on the 2 cell lines. Bombesin was secreted by all 4 cell lines during 24-hr culture in serum-free media, and its recovery was enhanced in the presence of protease inhibitors. Primer extension analysis demonstrated the presence of mRNA for both bombesin and its receptor in HPAF, CD18, CD11 and PANC-1 cells, even though no functional receptor was found in the latter 2 lines. Bombesin significantly stimulated the proliferation of HPAF and CD18 cells. This trophic effect was inhibited by the specific bombesin antagonist RC-3095. Bombesin may act as an autocrine growth factor in some human pancreatic cancer cell lines. Furthermore, other cell lines transcribe mRNA for bombesin receptors but have no functional bombesin receptors, suggesting a genetic or post-translational change in the receptor for these cells. Bombesin may be involved as a growth factor in the development of pancreatic ductal adenocarcinoma in humans. This possible autocrine growth pathway may provide an avenue for therapeutic intervention in this malignant disease. © 1996 Wiley-Liss, Inc.
Analysis of T cell subsets and beta chemokines in patients with pulmonary sarcoidosis (1997)

These results suggest a possible interaction between activated memory T cells bearing CD11a and RANTES which may contribute to the pulmonary involvement in patients with sarcoidosis.
Regulation of Immune Cells by Eicosanoid Receptors (2007)

Eicosanoids are potent, bioactive, lipid mediators that regulate important components of the immune response, including defense against infection, ischemia, and injury, as well as instigating and perpetuating autoimmune and inflammatory conditions. Although these lipids have numerous effects on diverse cell types and organs, a greater understanding of their specific effects on key players of the immune system has been gained in recent years through the characterization of individual eicosanoid receptors, the identification and development of specific receptor agonists and inhibitors, and the generation of mice genetically deficient in various eicosanoid receptors. In this review, we will focus on the receptors for prostaglandin D2, DP1 and DP2/CRTH2; the receptors for leukotriene B4, BLT1 and BLT2; and the receptors for the cysteinyl leukotrienes, CysLT1 and CysLT2, by examining their specific effects on leukocyte subpopulations, and how they may act in concert towards the development of immune and inflammatory responses.
Simulation and experimental studies on the concept of a rate-adaptive digital subscriber loop (RA-DSL) (1991)

The authors report simulation results and prototype control protocols for a digital subscriber loop transmission system, which will find and operate at the highest common bidirectional transmission rate that is viable on a given loop while preserving a specified noise margin. A prototype implements the rate-adaptation and transmission protocols over a captive multigauge cable facility. Simulation results predict the accompanying symbol rate versus reach characteristics for a transceiver with the same structure as basic rate access (BRA) systems under RA-DSL control. Results show that 1.5 Mb/s could be delivered to loops of up to 2 km while subscribers out to 10 km could receive 80 kb/s. For a number of specialized or short-notice situations, RA-DSL could be the basis for a fast and flexible response vehicle. If RA-DSL cannot serve an individual combination of distance and capacity, existing methods remain. However, a statistical assessment with metro population data shows the potential for RA-DSL to satisfy 4-6 times more n*DS-0 access requests than BRA on existing copper, without carrier serving area constraints.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The inheritance of virulence in Bremia lactucae to match resistance factors 3, 4, 5, 6, 8, 9, 10 and 11 in lettuce ( Lactuca sativa ) (1984)

The inheritance of virulence in Bremia lactucae to match specific resistance factors in lettuce was studied by crossing heterothallic isolates of B. lactucae. Avirulence seemed to be dominant to virulence. Although virulence to some R‐factors was inherited at a single locus, thus supporting the hypothesis of a gene‐for‐gene interaction between B. lactucae and L. sativa , inheritance of virulence to other R‐factors was more complex. Two loci seemed to determine virulence to R11; the determinants of virulence to R5, R8 and R10 were either closely linked or allelic; virulence to these loci appeared to be epistatic to virulence to match R9. Virulence to R4 probably involved the interaction of two loci, one of which inhibited avirulence. Determinants of fitness of B. lactucae and possibly genes of minor effect modifying specific virulence factors also segregated. These studies emphasized the potential variability in B. lactucae and implied that isolates should not be assigned to distinct races.
Use of Flutemetamol F 18–Labeled Positron Emission Tomography and Other Biomarkers to Assess Risk of Clinical Progression in Patients With Amnestic Mild Cognitive Impairment (2018)

<h3>Importance</h3> Patients with amnestic mild cognitive impairment (aMCI) may progress to clinical Alzheimer disease (AD), remain stable, or revert to normal. Earlier progression to AD among patients who were β-amyloid positive vs those who were β-amyloid negative has been previously observed. Current research now accepts that a combination of biomarkers could provide greater refinement in the assessment of risk for clinical progression. <h3>Objective</h3> To evaluate the ability of flutemetamol F 18 and other biomarkers to assess the risk of progression from aMCI to probable AD. <h3>Design, Setting, and Participants</h3> In this multicenter cohort study, from November 11, 2009, to January 16, 2014, patients with aMCI underwent positron emission tomography (PET) at baseline followed by local clinical assessments every 6 months for up to 3 years. Patients with aMCI (365 screened; 232 were eligible) were recruited from 28 clinical centers in Europe and the United States. Physicians remained strictly blinded to the results of PET, and the standard of truth was an independent clinical adjudication committee that confirmed or refuted local assessments. Flutemetamol F 18–labeled PET scans were read centrally as either negative or positive by 5 blinded readers with no knowledge of clinical status. Statistical analysis was conducted from February 19, 2014, to January 26, 2018. <h3>Interventions</h3> Flutemetamol F 18–labeled PET at baseline followed by up to 6 clinical visits every 6 months, as well as magnetic resonance imaging and multiple cognitive measures. <h3>Main Outcomes and Measures</h3> Time from PET to probable AD or last follow-up was plotted as a Kaplan-Meier survival curve; PET scan results, age, hippocampal volume, and aMCI stage were entered into Cox proportional hazards logistic regression analyses to identify variables associated with progression to probable AD. <h3>Results</h3> Of 232 patients with aMCI (118 women and 114 men; mean [SD] age, 71.1 [8.6] years), 98 (42.2%) had positive results detected on PET scan. By 36 months, the rates of progression to probable AD were 36.2% overall (81 of 224 patients), 53.6% (52 of 97) for patients with positive results detected on PET scan, and 22.8% (29 of 127) for patients with negative results detected on PET scan. Hazard ratios for association with progression were 2.51 (95% CI, 1.57-3.99;<i>P</i> &lt; .001) for a positive β-amyloid scan alone (primary outcome measure), 5.60 (95% CI, 3.14-9.98;<i>P</i> &lt; .001) with additional low hippocampal volume, and 8.45 (95% CI, 4.40-16.24;<i>P</i> &lt; .001) when poorer cognitive status was added to the model. <h3>Conclusions and Relevance</h3> A combination of positive results of flutemetamol F 18–labeled PET, low hippocampal volume, and cognitive status corresponded with a high probability of risk of progression from aMCI to probable AD within 36 months.
Recognizing emotion in speech (2002)

The paper explores several statistical pattern recognition techniques to classify utterances according to their emotional content. The authors have recorded a corpus containing emotional speech with over a 1000 utterances from different speakers. They present a new method of extracting prosodic features from speech, based on a smoothing spline approximation of the pitch contour. To make maximal use of the limited amount of training data available, they introduce a novel pattern recognition technique: majority voting of subspace specialists. Using this technique, they obtain classification performance that is close to human performance on the task.
Certain calcium channel blockers bind specifically to multidrug-resistant human KB carcinoma membrane vesicles and inhibit drug binding to P-glycoprotein. (1987)

The calcium channel blockers verapamil and diltiazem have been shown to reverse multidrug resistance, but the mechanism of action of these agents is still unknown. We measured [3H]verapamil, [3H]desmethoxyverapamil, [3H]diltiazem, and [3H]nitrendipine binding to membrane vesicles made from drug-sensitive (KB-3-1), multidrug-resistant (KB-C4 and KB-V1), and revertant (KB-V1-R2) cells. Membrane vesicles from KB-V1 cells bound 10-20-fold more [3H]verapamil and [3H]diltiazem and about 30-fold more [3H]desmethoxyverapamil than did vesicles from the parental KB-3-1 or revertant KB-V1-R2 cell lines. These drugs reverse the multidrug resistance phenotype by increasing accumulation of drugs in the resistant cells. No difference in binding of [3H]nitrendipine, which did not reverse drug resistance, was observed. The binding of vinblastine, desmethoxyverapamil, and diltiazem to KB-V1 vesicles was specific and saturable and was inhibited by desmethoxyverapamil and quinidine greater than vinblastine and diltiazem much greater than daunomycin. In addition, verapamil and diltiazem inhibited the vinblastine photoaffinity labeling of P170, the protein previously shown to be a marker of multidrug resistance.
EHMT1 and EHMT2 inhibition induces fetal hemoglobin expression (2015)

Fetal hemoglobin (HbF, α2γ2) induction is a well-validated strategy for sickle cell disease (SCD) treatment. Using a small-molecule screen, we found that UNC0638, a selective inhibitor of EHMT1 and EHMT2 histone methyltransferases, induces γ-globin expression. EHMT1/2 catalyze mono- and dimethylation of lysine 9 on histone 3 (H3K9), raising the possibility that H3K9Me2, a repressive chromatin mark, plays a role in silencing γ-globin expression. In primary human adult erythroid cells, UNC0638 and EHMT1 or EHMT2 short hairpin RNA-mediated knockdown significantly increased γ-globin expression, HbF synthesis, and the percentage of cells expressing HbF. At effective concentrations, UNC0638 did not alter cell morphology, proliferation, or erythroid differentiation of primary human CD34(+) hematopoietic stem and progenitor cells in culture ex vivo. In murine erythroleukemia cells, UNC0638 and Ehmt2 CRISPR/Cas9-mediated knockout both led to a marked increase in expression of embryonic β-globin genes Hbb-εy and Hbb-βh1. In primary human adult erythroblasts, chromatin immunoprecipitation followed by sequencing analysis revealed that UNC0638 treatment leads to genome-wide depletion in H3K9Me2 and a concomitant increase in the activating mark H3K9Ac, which was especially pronounced at the γ-globin gene region. In RNA-sequencing analysis of erythroblasts, γ-globin genes were among the most significantly upregulated genes by UNC0638. Further increase in γ-globin expression in primary human adult erythroid cells was achieved by combining EHMT1/2 inhibition with the histone deacetylase inhibitor entinostat or hypomethylating agent decitabine. Our data provide genetic and pharmacologic evidence that EHMT1 and EHMT2 are epigenetic regulators involved in γ-globin repression and represent a novel therapeutic target for SCD.
Orthogonal thiol–ene ‘click’ reactions: a powerful combination for fabrication and functionalization of patterned hydrogels (2017)

A combination of 'orthogonal' thiol-ene 'click' reactions is utilized for fabrication and functionalization of micro-patterned hydrogels. A furan-protected maleimide-containing parent copolymer is partially activated via the retro Diels-Alder reaction to obtain an 'orthogonally' functionalizable copolymer, where the different functional groups can be exploited for multi-functionalization or fabrication of functional hydrogels using combination of the nucleophilic and radical thiol-ene reactions.
NMR Structures of r(GCA

G

GC

G

UGC)2 and Determinants of Stability for Single Guanosine−Guanosine Base Pairs, (2000)

Nucleotides in RNA that are not Watson-Crick-paired form unique structures for recognition or catalysis, but determinants of these structures and their stabilities are poorly understood. A single noncanonical pair of two guanosines (G) is more stable than other noncanonical pairs and can potentially form pairing structures with two hydrogen bonds in four different ways. Here, the energetics and structure of single GG pairs are investigated in several sequence contexts by optical melting and NMR. The data for r(5'GCAGGCGUGC3')(2), in which G4 and G7 are paired, are consistent with a model in which G4 and G7 alternate syn glycosidic conformations in a two-hydrogen-bond pair. The two distinct structures are derived from nuclear Overhauser effect spectroscopic distance restraints coupled with simulated annealing using the AMBER 95 force field. In each structure, the imino and amino protons of the anti G are hydrogen bonded to the O6 and N7 acceptors of the syn G, respectively. An additional hydrogen-bond connects the syn G amino group to the 5' nonbridging pro-R(p) phosphate oxygen. The GG pair fits well into a Watson-Crick helix. In r(5'GCAGGCGUGC3')(2), the G4(anti), G7(syn) structure is preferred over G4(syn), G7(anti). For single GG pairs in other contexts, exchange processes make interpretation of spectra more difficult but the pairs are also G(syn), G(anti). Thermodynamic data for a variety of duplexes containing pairs of G, inosine, and 7-deazaguanosine flanked by GC pairs are consistent with the structural and energetic interpretations for r(5'GCAGGCGUGC3')(2), suggesting similar GG conformations.
The processing of peptide precursors (1986)

The classical conversion site in precursors of regulatory peptides is a sequence of two basic amino acids. During recent years, however, a group of monobasic cleavage sites has emerged. In certain cell systems it has been shown that the monobasic cleavage mechanism is both a specific mechanism which only attacks a particular basic residue, and a distinct mechanism which can be separated from the dibasic cleaving mechanism within the same cell. The vast majority of monobasic cleavages occur at single arginines although cleavage after a lysine residue has also been demonstrated. There is no ‘consensus sequence’ of amino acids surrounding the single basic residue which is the apparent signal for proteolytic processing. However, in approximately one third of the cases, a proline residue is found either just before or just after the basic residue. On the basis of this ‘proline‐directed arginyl cleavage’ it is discussed how the conformation of the peptide backbone might be important for this type of cleavage. Finally, it is suggested that tissue‐specific expression of different processing enzymes, e.g. dibasic and monobasic specific forms, might explain the tissue‐specific processing of precursors like the pro‐opiomelanocortin and the CKK. and somatostatin precursor.
Quantitative Proteomics Profiling of Primary Lung Adenocarcinoma Tumors Reveals Functional Perturbations in Tumor Metabolism (2013)

In this study, we have analyzed human primary lung adenocarcinoma tumors using global mass spectrometry to elucidate the biological mechanisms behind relapse post surgery. In total, we identified over 3000 proteins with high confidence. Supervised multivariate analysis was used to select 132 proteins separating the prognostic groups. Based on in-depth bioinformatics analysis, we hypothesized that the tumors with poor prognosis had a higher glycolytic activity and HIF activation. By measuring the bioenergetic cellular index of the tumors, we could detect a higher dependency of glycolysis among the tumors with poor prognosis. Further, we could also detect an up-regulation of HIF1α mRNA expression in tumors with early relapse. Finally, we selected three proteins that were upregulated in the poor prognosis group (cathepsin D, ENO1, and VDAC1) to confirm that the proteins indeed originated from the tumor and not from a stromal or inflammatory component. Overall, these findings show how in-depth analysis of clinical material can lead to an increased understanding of the molecular mechanisms behind tumor progression.
Phosphatidylinositol linkage of a truncated form of the platelet-derived growth factor receptor. (1988)

The platelet-derived growth factor (PDGF) receptor is usually anchored to the plasma membrane through a membrane-spanning hydrophobic amino acid sequence that splits the molecule into two approximately equal pieces, an amino-terminal external domain that contains the binding site for PDGF and a carboxyl-terminal cytoplasmic domain that includes the tyrosine kinase coding sequences. Here we report the expression of a truncated PDGF receptor that consists of the extracellular domain without the transmembrane and cytoplasmic domains. Unexpectedly, this form of the receptor that lacks a hydrophobic membrane-anchoring sequence was bound to the membrane and was not secreted into the culture media. Conventional methods to dissociate noncovalent protein-protein interactions failed to release the protein from the membrane. When the transmembrane and cytoplasmic sequences were artificially deleted from the PDGF receptor, the truncated extracellular domain was anchored to the membrane through phospholipids and could be released by phospholipase C treatment. This truncated form of the receptor bound PDGF with an affinity 5-20-fold lower than the full-length receptor.
Inhibitory effect of clopidogrel on platelet adhesion and intimal proliferation after arterial injury in rabbits. (1993)

The possible activity of ticlopidine and its analogue clopidogrel in early atherogenesis was investigated. Incubation of rabbit platelets with the extracellular matrix produced by endothelial cells in culture induced massive platelet adherence in vitro. This phenomenon was strongly reduced when platelets were isolated from rabbits that had been treated with a single dose of clopidogrel (10 mg/kg PO) or three doses of ticlopidine (each 200 mg/kg PO) (94% and 56% inhibition of platelet adhesion, respectively). Three doses of aspirin (each 200 mg/kg PO) were ineffective. Air-drying injury of the rabbit carotid artery resulted in platelet adherence to the underlying subendothelium. This platelet accumulation on the damaged vessel wall was greatly reduced by clopidogrel: 95% (P < .001) inhibition of platelet adhesion after a single oral dose of 25 mg/kg. Ticlopidine (200 mg/kg) was also effective (71% inhibition; P < .001), whereas aspirin (100 mg/kg PO) failed to reduce platelet adhesion to the subendothelium. The effect of clopidogrel on intimal smooth muscle hyperplasia in rabbit carotid arteries subjected to air-drying endothelial injury was then investigated. After a 16-day treatment, clopidogrel (25 mg/kg per day PO) inhibited the development of intimal thickening (48% inhibition; P < .01). This effect was dose dependent and increased with the duration of the treatment. Under the same experimental conditions, ticlopidine (200 mg/kg per day PO) inhibited myointimal thickening (57%; P < .001), whereas aspirin was ineffective. These results show that clopidogrel and ticlopidine, two ADP-selective antiplatelet agents, can reduce myointimal thickening after endothelial injury. This effect can be due to the inhibition of platelet adhesion and aggregation to the exposed subendothelium.