gebhart/patrepeval huggingface dataset:
N4-Unsubstituted N1-Arylpiperazines as High-Affinity 5-HT1A Receptor Ligands (1995)

In order to explore the structural requirements for high 5-HT1A affinity, a series of aryl-substituted N1-phenylpiperazines were synthesized and evaluated for their ability to displace [3H]-8-OH-DPAT from its specific binding sites in rat frontal cortex homogenates. We found 2-methoxy substitution to be favorable, while 4-methoxy substitution was detrimental for 5-HT1A affinity. Substitution with annelated rings at the 2,3-positions was highly favorable for all investigated compounds, with the exception of a pyrrole ring. All other substitutions, except fluoro, in this class of heterobicyclic phenylpiperazines decreased affinity in the order: ortho > para > meta. The loss of affinity in the ortho and para positions is probably due to steric factors: the substituents either cause steric hindrance with the receptor or prevent the compound from adopting the appropriate conformation for binding to the 5-HT1A receptor. Conformational analysis combined with structure-affinity relationships (SAR) indicates that our arylpiperazines may bind at the 5-HT1A receptor in a nearly coplanar conformation. Observed interactions of the compounds in our 5-HT1A receptor model appeared to be in agreement with SAR data. The aromatic part of the arylpiperazine moiety has pi-pi interactions with the aromatic residues Trp161 and Phe362 in helices IV and VI, respectively. The positively charged protonated basic nitrogen forms a hydrogen bond with the negatively charged Asp116 in helix III. The ammonium-aspartate complex is surrounded by aromatic residues Trp358 and Phe361 in helix VI. A lipophilic pocket is formed by Phe362, Leu366 (both helix VI), and the methyl group of Thr200 (helix V). In agreement with the model, addition of a methyl substituent to the structure of the benzodioxine analogue 12 in this region, yielding 13, is favorable for 5-HT1A receptor affinity. Unfavorable positions for substitution with bulky groups, like the 3- and 4-positions in the benzofuran compound 14, are explained by steric hindrance with the backbone atoms of helix V. Thus, we were able to rationalize the 5-HT1A SAR of existing N1-phenylpiperazines, as well as a series of newly synthesized bicyclic heteroarylpiperazines, in terms of receptor-ligand interactions. Several of these N4-unsubstituted compounds had affinities in the low-nanomolar range.
Active vaccination with Dickkopf-1 induces protective and therapeutic antitumor immunity in murine multiple myeloma (2011)

Dickkopf-1 (DKK1), broadly expressed in myeloma cells but highly restricted in normal tissues, together with its functional roles as an osteoblast formation inhibitor, may be an ideal target for immunotherapy in myeloma. Our previous studies have shown that DKK1 (peptide)-specific CTLs can effectively lyse primary myeloma cells in vitro. The goal of this study was to examine whether DKK1 can be used as a tumor vaccine to elicit DKK1-specific immunity that can control myeloma growth or even eradicate established myeloma in vivo. We used DKK1-DNA vaccine in the murine MOPC-21 myeloma model, and the results clearly showed that active vaccination using the DKK1 vaccine not only was able to protect mice from developing myeloma, but it was also therapeutic against established myeloma. Furthermore, the addition of CpG as an adjuvant, or injection of B7H1-blocking or OX40-agonist Abs, further enhanced the therapeutic effects of the vaccine. Mechanistic studies revealed that DKK1 vaccine elicited a strong DKK1- and tumor-specific CD4+ and CD8+ immune responses, and treatment with B7H1 or OX40 Abs significantly reduced the numbers of IL-10-expressing and Foxp3+ regulatory T cells in vaccinated mice. Thus, our studies provide strong rationale for targeting DKK1 for immunotherapy of myeloma patients.
Aldehyde Selective Wacker Oxidations of Phthalimide Protected Allylic Amines: A New Catalytic Route to β3-Amino Acids (2009)

A new method for the synthesis of beta(3)-amino acids is presented. Phthalimide protected allylic amines are oxidized under Wacker conditions selectively to aldehydes using PdCl(2) and CuCl or Pd(MeCN)(2)Cl(NO(2)) and CuCl(2) as complementary catalyst systems. The aldehydes are produced in excellent yields and exhibit a large substrate scope. Beta-amino acids and alcohols are synthesized by oxidation or reduction and subsequent deprotection.
MatGAT: An application that generates similarity/identity matrices using protein or DNA sequences (2003)

The advantages of this program over other software are that it is open-source freeware, can analyze a large number of sequences simultaneously, can visualize both sequence alignment and similarity/identity values concurrently, employs global alignment in calculations, and has been formatted to run under both the Unix and the Microsoft Windows Operating Systems. We are presently completing the Macintosh-based version of the program.
Dendrite‐Assisted Growth of Silicon Nanowires in Electroless Metal Deposition (2003)

Abstract This article concerns the detailed investigations on the silver dendrite‐assisted growth of single‐crystalline silicon nanowires, and their possible self‐assembling nanoelectrochemistry growth mechanism. The growth of silicon nanowires was carried out through an electroless metal deposition process in a conventional autoclave containing aqueous HF and AgNO 3 solution near room temperature. In order to explore the mechanism and prove the centrality of silver dendrites in the growth of silicon nanowires, other etching solution systems with different metal species were also investigated in this work. The morphology of etched silicon substrates strongly depends upon the composition of the etching solution, especially the metal species. Our experimental results prove that the simultaneous formation of silver dendrites is a guarantee of the preservation of free‐standing nanoscale electrolytic cells on the silicon substrate, and also assists in the final formation of silicon nanowire arrays on the substrate surface.
Synergistic interaction between interleukin 4 and anti‐Bp50 (CDw40) revealed in a novel B cell restimulation assay (1987)

Highly purified resting B lymphocytes stimulated for 3 days to high-rate DNA synthesis by a synergistic combination of phorbol dibutyrate and ionomycin soon returned to quiescence once those signals had been removed. The maintenance of DNA synthesis in such cultures was found to provide a sensitive assay for revealing the factors that interact with cycling B cells. Whereas several activities-namely, interleukin 4, anti-Bp50 and a low molecular weight B cell growth factor-were, by themselves, capable of prolonging DNA synthesis over a further day or so, no single factor was capable of sustaining the replication cycle out to day 6 of culture. By contrast, certain combinations of activities displayed significant synergy in the restimulation assay. The most striking observed was that between interleukin 4 and anti-Bp50 where, by day 6, their combined effect on maintaining DNA synthesis in 3-day stimulated cells was the same as having kept phorbol dibutyrate and ionomycin in the culture system. The implications of these findings are discussed.
Collectins and Ficolins: Humoral Lectins of the Innate Immune Defense (2003)

Collectins and ficolins, present in plasma and on mucosal surfaces, are humoral molecules of the innate immune systems, which recognize pathogen-associated molecular patterns. The human collectins, mannan-binding lectin (MBL) and surfactant protein A and D (SP-A and SP-D), are oligomeric proteins composed of carbohydrate-recognition domains (CRDs) attached to collagenous regions and are thus structurally similar to the ficolins, L-ficolin, M-ficolin, and H-ficolin. However, they make use of different CRD structures: C-type lectin domains for the collectins and fibrinogen-like domains for the ficolins. Upon recognition of the infectious agent, MBL and the ficolins initiate the lectin pathway of complement activation through attached serine proteases (MASPs), whereas SP-A and SP-D rely on other effector mechanisms: direct opsonization, neutralization, and agglutination. This limits the infection and concurrently orchestrates the subsequent adaptive immune response. Deficiencies of the proteins may predispose to infections or other complications, e.g., reperfusion injuries or autoimmune diseases. Structure, function, clinical implications, and phylogeny are reviewed.
Expression of the insulin-like growth factor 1 receptor (IGF-1R) in breast cancer cells: evidence for a regulatory role of dolichyl phosphate in the transition from an intracellular to an extracellular IGF-1 pathway (1999)

In this study we provide evidence that the low expression of IGF-1R at the cell surface of estrogen-independent breast cancer cells is due to a low rate of de novo synthesis of dolichyl phosphate. The analyses were performed on the estrogen receptor-negative breast cancer cell line MDA231 and, in comparison, the melanoma cell line SK-MEL-2, which expresses a high number of plasma membrane-bound IGF-1R. Whereas the MDA231 cells had little or no surface expression of IGF-1R, they expressed functional (i.e., ligand-binding) intracellular receptors. By measuring the incorporation of [3H]mevalonate into dolichyl phosphate, we could demonstrate that the rate of dolichyl phosphate synthesis was considerably lower in MDA231 cells than in SK-MEL-2 cells. Furthermore, N-linked glycosylation of the alpha-subunit of IGF-1R was 8-fold higher in the melanoma cells. Following addition of dolichyl phosphate to MDA231 cells, N-linked glycosylation of IGF-1R was drastically increased, which in turn was correlated to a substantial translocation of IGF-1R to the plasma membrane, as assayed by IGF-1 binding analysis and by Western blotting of plasma membrane proteins. The dolichyl phosphate-stimulated receptors were proven to be biochemically active since they exhibited autophosphorylation. Under normal conditions MDA231 cells, expressing very few IGF-1R at the cell surface, were not growth-arrested by an antibody (alphaIR-3) blocking the binding of IGF-1 to IGF-1R. However, after treatment with dolichyl phosphate, leading to a high cell surface expression of IGF-1R, alphaIR-3 efficiently blocked MDA231 cell growth. Taken together with the fact that the breast cancer cells produce IGF-1 and exhibit intracellular binding, our data suggest that the level of de novo -synthesized dolichyl phosphate may be critical for whether the cells will use an intracellular or an extracellular autocrine IGF-1 pathway.
Regenerative Nd:glass amplifier seeded with a Nd:fiber laser (1992)

Wavelength tuning and broad-bandwidth operation of a passively mode-locked Nd:fiber laser is demonstrated at 1060 microm. The oscillator pulses are used to seed a bulk regenerative Nd:glass amplifier, and 300-fs transformlimited pulses with an energy of 10 microJ are obtained after 31 round trips at a repetition rate of 500 Hz.
Interactions of porphyrins with nucleic acids (1983)

The interactions of tetrakis(4-N-methylpyridyl)-porphine (H2TMpyP-4) and its copper(II), nickel(II), zinc(II), cobalt(III), iron(III), and manganese(III) derivatives with several nucleic acids have been investigated. Spectrophotometric titrations of H2TMpyP-4 and Cu(II)TMpyP-4 with the synthetic polymer poly(dG-dC) could be analyzed by a nearest-neighbor exclusion model leading to n approximately equal to two base pairs and equilibrium constants of 7.7 X 10(5) M-1 and 8.0 X 10(5) M-1, respectively. The other metal derivatives [except for the nickel(II) porphyrin] do not provide sufficiently large color changes with poly(dG-dC) to allow analysis. In contrast, all of these porphyrins interact with poly(dA-dT) and DNA. For those porphyrins investigated, the binding profiles are not adequately fit by a nearest-neighbor exclusion model but have profiles suggesting that cooperativity effects are important. Spectral and circular dichroic experiments both suggest base specificity. With calf thymus DNA, the copper(II) and nickel(II) derivatives show prominent negative circular dichroism (CD) features and large red shifts and hypochromicity of the Soret absorption band characteristic of GC specificity, as demonstrated with the synthetic polymer. The other metal derivatives show prominent positive induced visible CD features with small red shifts and hypochromicity of the absorption bands in the Soret region characteristic of AT specificity. Only the metal-free derivative has a conservative CD spectrum suggesting distribution among GC and AT sites.
Optical free-form surfaces in off-axis head-worn display design (2008)

Head-worn displays are becoming a viable visual display option for mobile augmented reality. In this paper, we highlight the challenges and some recent progress towards compact and lightweight head-worn displays tending towards the eyeglass form factor. Single and dual-element eyeglass display designs that leverage the advances in free-form optics fabrication technology will be presented. There are three new contributions in this paper: first, we present a single-element eyeglass display design and the fabricated mirror prototype; second, we present our second generation dual-element eyeglass display design with the revised opto-mechanical packaging; third, we present our initial studies on the field of view limit with an 8 mm pupil for the dual-element design.
Ureaplasma urealyticum and Premature Birth (1993)

Evidence related to the association of Ureaplasma urealyticum with premature birth is reviewed. U. urealyticum is a common inhabitant in the vagina of pregnant women. It is recovered from the vaginas of approximately 70% of pregnant women. The presence of U. urealyticum in the vagina is not associated with premature birth. Therapy to eradicate U. urealyticum from the vagina during pregnancy does not reduce the incidence of premature birth. Recovery of U. urealyticum from the amniotic fluid has not been associated with prematurity. However, in three of six reports, the recovery of U. urealyticum from the chorioamnion has been associated with prematurity, and U. urealyticum is rather consistently associated with histological chorioamnionitis. This review suggests that U. urealyticum in the lower genital tract is not associated with premature birth but that its presence in the chorioamnion is weakly associated with prematurity and strongly associated with histological chorioamnionitis.
Strong Resistance of Phosphorylcholine Self-Assembled Monolayers to Protein Adsorption:  Insights into Nonfouling Properties of Zwitterionic Materials (2005)

In this work, we show the strong resistance of zwitterionic phosphorylcholine (PC) self-assembled monolayers (SAMs) to protein adsorption and examine key factors leading to their nonfouling behavior using both experimental and molecular simulation techniques. Zwitterions with a balanced charge and minimized dipole are excellent candidates as nonfouling materials due to their strong hydration capacity via electrostatic interactions.
Effect of kappa opioid agonists on visceral nociception induced by uterine cervical distension in rats (2002)

Although uterine distension in rats results in an escape reflex, there exists no model of uterine cervical distension (UCD), the pain stimulus during the first stage of labor. The aims of this study were to develop such a model in virgin rats and to test whether peripherally restricted kappa opioid receptor (KOR) agonists (ADL 10-0101, ADL 10-0102, ADL 10-0116) inhibit responses to UCD. Under intravenous (i.v.) pentobarbital and alpha-chloralose anesthesia, fine metal rods were inserted in both uterine cervical osses through a small midline laparotomy. UCD was performed by manual separation of the rods (25-100 g). Single-unit afferent responses in hypogastric nerve or reflex rectus abdominis electromyographic (EMG) activity were determined before and after i.v. KOR agonists. UCD resulted in a stimulus-dependent increase in single-unit afferent activity. Units could be characterized as low threshold (mean threshold 6.6+/-2.7 g), or high threshold (mean threshold 55+/-8.8 g); all were C fibers, all responded to topical bradykinin. ADL 10-0116 (10 mg/kg) reduced the afferent response to UCD. Reflex EMG response occurred over a distension force range of 25-100 g, unaffected by i.v. saline. All three KOR agonists produced a dose-dependent, naloxone-reversible inhibition of the EMG response with a potency relationship of ADL 10-0102 (ED50 0.04 mg/kg)>ADL 10-0101 (ED50 0.65 mg/kg)=ADL 10-0116 (ED50 0.60 mg/kg). These data support the use of acute UCD as a noxious stimulus, inducing afferent and reflex activity. Like other visceral stimuli, UCD is sensitive to inhibition by KOR agonists.
Selective depletion of alloreactive donor lymphocytes: a novel method to reduce the severity of graft-versus-host disease in older patients undergoing matched sibling donor stem cell transplantation (2005)

We have selectively depleted host-reactive donor T cells from peripheral blood stem cell (PBSC) transplant allografts ex vivo using an anti-CD25 immunotoxin. We report a clinical trial to decrease graft-versus-host disease (GVHD) in elderly patients receiving selectively depleted PBSC transplants from HLA-identical sibling donors. Sixteen patients (median age, 65 years [range, 51-73 years]), with advanced hematologic malignancies underwent transplantation following reduced-intensity conditioning with fludarabine and either cyclophosphamide (n = 5), melphalan (n = 5), or busulfan (n = 6). Cyclosporine was used as sole GVHD prophylaxis. The allograft contained a median of 4.5 x 10(6) CD34 cells/kg (range, 3.4-7.3 x 10(6) CD34 cells/kg) and 1.0 x 10(8)/kg (range, 0.2-1.5 x 10(8)/kg) selectively depleted T cells. Fifteen patients achieved sustained engraftment. The helper T-lymphocyte precursor (HTLp) frequency assay demonstrated successful (mean, 5-fold) depletion of host-reactive donor T cells, with conservation of third-party response in 9 of 11 cases tested. Actuarial rates of acute GVHD were 46% +/- 13% for grades II to IV and 12% +/- 8% for grades III to IV. These results suggest that allodepletion of donor cells ex vivo is clinically feasible in older patients and may reduce the rate of severe acute GVHD. Further studies with selectively depleted transplants to evaluate graft-versus-leukemia (GVL) and survival are warranted.
Exploring meat substitutes: consumer experiences and contextual factors (2013)

Purpose Meat substitutes can be environmentally more sustainable alternatives to meat. However, the image of these products in The Netherlands is still low. The purpose of this paper is to explore consumers' experiences and sensory expectations of meat substitutes and the appropriateness of the use of meat substitutes in meals. Design/methodology/approach In total, 46 consumers took part in seven focus group discussions. These discussions consisted of three steps, starting with a general discussion on meat substitutes, followed by a discussion on the appropriateness of the use of meat substitutes as ingredients (minced, in pieces or slices) by using photographs of six different dishes (soup, pasta, rice, wrap, meal salad, and pizza). The discussions were concluded with a taste session of two dishes with meat substitutes. Findings Consumers in this study regarded health aspects and easy preparation as positive aspects of meat substitutes. Lack of information on the package, and high price were reported as negative. Sensory aspects such as neutral taste or tastiness, crispiness, chicken‐like texture, or granular texture were seen as positive attributes. Negative sensory aspects that were mentioned were uniform taste, compactness, dryness and softness. Most consumers found the use of meat substitutes appropriate in the dishes we presented. Originality/value The paper's findings can, together with quantitative consumer and sensory research, be a start towards consumer‐oriented product development of environmentally more sustainable meat substitutes. The central role of meal context and appropriateness is an aspect that has not yet received much attention in food science.
Eicosapentaenoic and docosapentaenoic acids are the principal products of α-linolenic acid metabolism in young men (2002)

The capacity for conversion of alpha-linolenic acid (ALNA) to n-3 long-chain polyunsaturated fatty acids was investigated in young men. Emulsified [U-13C]ALNA was administered orally with a mixed meal to six subjects consuming their habitual diet. Approximately 33 % of administered [13C]ALNA was recovered as 13CO2 on breath over the first 24 h. [13C]ALNA was mobilised from enterocytes primarily as chylomicron triacylglycerol (TAG), while [13C]ALNA incorporation into plasma phosphatidylcholine (PC) occurred later, probably by the liver. The time scale of conversion of [13C]ALNA to eicosapentaenoic acid (EPA) and docosapentaenoic acid (DPA) suggested that the liver was the principal site of ALNA desaturation and elongation, although there was some indication of EPA and DPA synthesis by enterocytes. [13C]EPA and [13C]DPA concentrations were greater in plasma PC than TAG, and were present in the circulation for up to 7 and 14 d, respectively. There was no apparent 13C enrichment of docosahexaenoic acid (DHA) in plasma PC, TAG or non-esterified fatty acids at any time point measured up to 21 d. This pattern of 13C n-3 fatty acid labelling suggests inhibition or restriction of DHA synthesis downstream of DPA. [13C]ALNA, [13C]EPA and [13C]DPA were incorporated into erythrocyte PC, but not phosphatidylethanolamine, suggesting uptake of intact plasma PC molecules from lipoproteins into erythrocyte membranes. Since the capacity of adult males to convert ALNA to DHA was either very low or absent, uptake of pre-formed DHA from the diet may be critical for maintaining adequate membrane DHA concentrations in these individuals.
Increased Intestinal Permeability Associated With Infection in Burn Patients (1988)

Thermal injury may be associated with disruption of normal gut barrier integrity. To test this hypothesis, we assessed intestinal permeability with the nonmetabolizable, poorly absorbed disaccharide lactulose, which is efficiently excluded by the normal intestinal mucosa. Permeability studies were performed in 15 burned patients (aged 18 to 67 years; mean burn size, 40%) and 11 healthy controls. Lactulose, 10 g, was administered enterally, together with 5 g of mannitol as a control, and urinary excretion rates were determined. Lactulose excretion and the lactulose/mannitol excretion ratio increased threefold (160 +/- 30 vs 57 +/- 7 mumol and 0.113 +/- 0.033 vs 0.035 +/- 0.005) in the infected patients (sepsis score, 10 +/- 2; burn size, 38% +/- 6%). In contrast, noninfected burn patients (sepsis score, 0) had permeability values similar to those of controls (66 +/- 10 mumol and 0.036 +/- 0.007). Permeability increased as the severity of infection increased. Infection in burn patients is associated with increased bowel permeability. The intestine may be a primary source of sepsis. Alternatively, the systemic response to infection may alter gut barrier function, which could facilitate translocation of bacteria and absorption of endotoxin.