gebhart/patrepeval huggingface dataset:
Synthese von C‐2‐analogen Taxolen (1994)

Regioselektiv führt die nucleophile Ringöffung cyclischer Carbonate 1 zum weniger substituierten Ester 2 . Bei Molekülen mit mehreren Carbonylgruppen ist die Reaktion zudem chemoselektiv: Bei einer Taxol‐Vorstufe wurde die Carbonatgruppe und nicht eine der drei weiteren Carbonylgruppen angegriffen; die gebildeten Ester wurden zu unterschiedlich cytotoxischen Taxol‐Analoga umgesetzt. magnified image
Effect of chemical structure on physical properties of isomeric polyesters (1952)

Abstract It has been shown that changes in chemical structure of aromatic polyesters have a pronounced effect on the melting points and crystallinity of the polymers. Changes which remove the carboxyl group from the ring result in marked lowering of the melting point and toughness of the polymers. Changes which separate aromatic nuclei lower melting point but not as markedly as the above change. Changes which put an odd number of atoms in the polymer chain markedly lower the melting point. Changes which interfere with the possibility of co‐planarity of the components very markedly affect the crystallinity, and to a lesser extent the sticking point of polymers.
Impact of tobacco smoke on upper airway dendritic cell accumulation and regulation by sinonasal epithelial cells (2017)

Active smoking, and to a lesser degree ETS, alters the sinonasal composition of DCs. A potential mechanism to account for this is that cigarette smoke stimulates HSNECs to induce moDC migration, maturation, and activation.
Room Temperature Plasticity of Zr<sub>65</sub>Al<sub>7.5</sub>Ni<sub>10</sub>Cu<sub>17.5-x</sub>Pd<sub>x</sub> Bulk Metallic Glasses (2007)

Monolithic Zr65Al7.5Ni10Pd17.5 and Zr65Al7.5Ni10Cu17.5 hardly had plastic deformability in tension at room temperature, although Zr65Al7.5Ni10Pd17.5 showed a large plastic strain in compression. A depressed zone that is the evidence of viscous flow deformation (so-called viscous flow depression zone; VFD-zone) was observed for Zr65Al7.5Ni10Pd17.5 around the edge at the point of failure on its specimen surfaces. However, no VFD-zone was seen for Zr65Al7.5Ni10Cu17.5. Thus, a clear difference in tensile plastic behavior was found between Zr65Al7.5Ni10Pd17.5 and Zr65Al7.5Ni10Cu17.5. A structural change in the vicinity of the fracture surface of Zr65Al7.5Ni10Pd17.5 was measured by micro-beam X-ray diffractometry (MB-XRD). We may be able to discuss the room temperature plasticity of Zr65Al7.5Ni10Cu17.5-xPdx bulk metallic glasses correlating with the phase stability of the amorphous and icosahedral quasi-crystalline phases.
Combination of proton pump inhibitor and rebamipide, a free radical scavenger, promotes artificial ulcer healing after endoscopic submucosal dissection with dissection size >40 mm (2012)

In our previous study, the healing effect of proton pump inhibitor plus rebamipide for endoscopic submucosal dissection-related artificial ulcer smaller than 40 mm showed statistical significance. However, such effect of the combination was not yet clear for ulcers with dissected diameter more than 40 mm. The aim of this present study was to resolve this problem under sufficient statistical power, with adequate sample size. We conducted a randomized controlled study. Either the proton pump inhibitor mono-therapy or the combination therapy was prescribed for 28 days after endoscopic submucosal dissection. Eighty-seven patients were eligible for outcome evaluation. Combination therapy was significantly superior to mono-therapy, 27.8% vs 0% reached healing stage (scar stage) in cases with ulcers of dissection diameter more than 40 mm. In conclusion, the combination therapy with rebamipide was favorable regimen in patients with larger artificial ulcer after endoscopic submucosal dissection.
Driver Inattention Detection based on Eye Gaze—Road Event Correlation (2009)

Current road safety initiatives are approaching the limit of their effectiveness in developed countries. A paradigm shift is needed to address the preventable deaths of thousands on our roads. Previous systems have focused on one or two aspects of driving: environmental sensing, vehicle dynamics or driver monitoring. Our approach is to consider the driver and the vehicle as part of a combined system, operating within the road environment. A driver assistance system is implemented that is not only responsive to the road environment and the driver's actions but also designed to correlate the driver's eye gaze with road events to determine the driver's observations. Driver observation monitoring enables an immediate in-vehicle system able to detect and act on driver inattentiveness, providing the precious seconds for an inattentive human driver to react. We present a prototype system capable of estimating the driver's observations and detecting driver inattentiveness. Due to the “look but not see” case it is not possible to prove that a road event has been observed by the driver. We show, however, that it is possible to detect missed road events and warn the driver appropriately.
The Five Points Pose Problem : A New and Accurate Solution Adapted to any Geometric Configuration (2008)

The goal of this paper is to estimate directly the rotation and translation between two stereoscopic images with the help of five homologous points. The methodology presented does not mix the rotation and translation parameters, which is comparably an important advantage over the methods using the well-known essential matrix. This results in correct behavior and accuracy for situations otherwise known as quite unfavorable, such as planar scenes, or panoramic sets of images (with a null base length), while providing quite comparable results for more "standard" cases. The resolution of the algebraic polynomials resulting from the modeling of the coplanarity constraint is made with the help of powerful algebraic solver tools (the Groebner bases and the Rational Univariate Representation).
Identification of the receptor for erythropoietin by cross-linking to Friend virus-infected erythroid cells. (1987)

Erythropoietin (Epo) is a glycoprotein hormone that regulates erythroid development and interacts with surface receptors on developing erythroid cells. In this laboratory, a cell system with a relatively pure population of erythroid cells that respond to Epo has been developed. Immature erythroid cells are obtained from the spleens of mice infected with the anemia strain of Friend virus. The binding of 125I-labeled Epo (125I-Epo) to plasma membranes from these cells was studied in this investigation. 125I-Epo binding reached equilibrium within 20 min at 37 degrees C. Twenty percent of the receptors bound 125I-Epo with a Kd of 0.08 X 10(-9) M, while the remaining receptors bound the hormone with a Kd of 0.6 X 10(-9) M. In this study, a receptor for Epo was identified by cross-linking 125I-Epo to the receptor in intact cells and plasma membrane preparations using disuccinimidyl suberate. Polyacrylamide gel electrophoresis revealed two labeled bands of 100 and 85 kDa. The 85-kDa band was more heavily labeled (65%) than the 100-kDa band. Both bands were equally decreased when increasing amounts of unlabeled Epo were included in the binding mixture, indicating a specific interaction of 125I-Epo with the receptor.
Secondary Structure Estimation of Proteins Using the Amide III Region of Fourier Transform Infrared Spectroscopy: Application to Analyze Calcium-Binding-Induced Structural Changes in Calsequestrin (1994)

A Fourier transform infrared spectroscopic method has been developed to analyze protein secondary structure by employing the amide III spectral region (1350–1200 cm −1 )· Benefits of using the amide III region have been shown to be substantial. The interference from the water vibration (∼1640 cm −1 ) in the amide I region can be avoided when one is using the amide III band; furthermore, the amide III region also presents a more characterized spectral feature which provides easily resolved and better defined bands for quantitative analysis. Estimates of secondary structure are accomplished with the use of Fourier self-deconvolution, second derivatization, and curve-fitting on original protein spectra. The secondary structure frequency windows (α-helix, 1328–1289 cm −1 ; unordered, 1288–1256 cm −1 ; and β-sheets, 1255–1224 cm −1 ) have been obtained, and estimates of secondary structural contents are consistent with X-ray crystallography data for model proteins and parallel results obtained with the use of the amide I region. We have further applied the analysis to the structural change of calsequestrin upon Ca 2+ binding. Treatment of calsequestrin with 1 mM Ca 2+ results in the formation of crystalline aggregates accompanied by a 10% increase in α-helical structure, which is consistent with previous results obtained by Raman spectroscopy. Thus the amide III region of protein IR spectra appears to be a valuable tool in estimating individual protein secondary structural contents.
Reversible Control of Gelatin Hydrogel Stiffness Using DNA Crosslinkers (2020)

Biomaterials with dynamically tunable properties are critical for a range of applications in regenerative medicine and basic biology. In this work, we show the reversible control of gelatin methacrylate (GelMA) hydrogel stiffness through the use of DNA crosslinkers. We replaced some of the inter-GelMA crosslinks with double-stranded DNA, allowing for their removal via toehold-mediated strand displacement. The crosslinks could be restored by adding fresh dsDNA with complementary handles to the hydrogel. The elastic modulus (G’) of the hydrogels could be tuned between 500 and 1000 Pa, reversibly, over two cycles without degradation of performance. By functionalizing the gels with a second DNA strand, it was possible to control the crosslink density and a model ligand in an orthogonal fashion with two different displacement strands. Our results demonstrate the potential for DNA to reversibly control both stiffness and ligand presentation in a protein-based hydrogel, and will be useful for teasing apart the spatiotemporal behavior of encapsulated cells.
Modulation and instability in the sound of plastic soprano recorders (2017)

Soprano recorders are among the most popular wind instruments in music education for children. As these instruments are played by amateurs, they should be easy to play even by beginner players. The investigations reported in this paper were initiated by an instrument maker company. It was found that their plastic soprano recorders often had unsatisfactory sound quality and exhibited hard playability and strange, unstable steady state sounds, especially in the low regime. The experiments reported here were performed in order to examine the characteristic properties of these unusual sounds and to identify the background causes of the observed phenomena. In this contribution the results of various measurements carried out on different plastic soprano recorders are presented. Recorder sounds and edge tones are analyzed in the steady and attack transient states and their key properties are compared. The observed instabilities, strong amplitude modulations and the appearance of subharmonic components in the steady state sound are discussed. Finally, possible physical explanations of the experimental results are examined.
Design of Nontoxic Analogues of Cathelicidin-Derived Bovine Antimicrobial Peptide BMAP-27: The Role of Leucine as Well as Phenylalanine Zipper Sequences in Determining Its Toxicity (2009)

BMAP-27 is a cathelicidin-derived bovine antimicrobial peptide, which shows moderate cytotoxicity and potent antibacterial activity against a wide variety of microorganisms. Despite a number of studies, very little is known about the amino acid sequences of this peptide that controls its antibacterial and cytotoxic activities. Small stretches of phenylalanine and leucine zipper sequences were identified at the N- and C-termini of the molecule, respectively. To understand the structural and functional roles of these sequence elements, we synthesized and characterized several analogues of BMAP-27 after substituting leucine or phenylalanine residue(s) at a and/or d positions of the leucine and phenylalanine zipper sequences, respectively, with alanine. BMAP-27 analogues exhibited significantly reduced cytotoxicity against the human red blood (hRBC) and murine 3T3 cells as compared to that of the wild-type peptide. Interestingly, BMAP-27 and its analogues exhibited comparable antibacterial activity against the selected Gram-positive and Gram-negative bacteria. Moreover, BMAP-27 and its analogues exhibited similar localization and assembly onto the selected bacteria and induced comparable permeability in these cells. However, only BMAP-27, not its analogues, assembled and bound strongly onto the hRBCs and permeabilized them. The results indicated that not only a leucine zipper but also a phenylalanine zipper sequence plays an important role in maintaining the assembly of BMAP-27 on the mammalian cells examined here and cytotoxic activity against them. To the best of our knowledge, this is the first report of the evaluation of structural and functional roles of a phenylalanine zipper sequence in a naturally occurring antimicrobial peptide.
Palladium-catalysed cross-coupling of organosilicon reagents (2011)

The palladium catalysed cross-coupling of organosilicon reagents with organo halides and pseudo-halides has developed over the past 30 years into an efficient and attractive carbon-carbon bond forming strategy. Extensive research within this field to expand and diversify on the scope of the organosilicon coupling reaction will continue to promote its use in the synthesis of biologically and pharmaceutically important organic molecules. The recent advances made within this area are explored in this critical review (199 references).
Easy Strategy To Protect Antimicrobial Peptides from Fast Degradation in Serum (2010)

Antimicrobial peptides are promising novel peptide leads, but their low serum stability often limits their further consideration in drug development programs. Here, we describe a generally applicable strategy to stabilize peptides against serum proteases by replacing arginine residues with alpha-amino-3-guanidino-propionic acid (Agp). Peptide NH(2)-RRWRIVVIRVRR-CONH(2) was nearby totally degraded after 8 h in mouse serum, whereas the variant with Agp substituted was degraded less than 20%. The antimicrobial activity was not affected.
Label-free hyperspectral microscopy for scatter imaging of biological processes in cells(Conference Presentation) (2016)

We will present unique applications of a label-free, hyperspectral scatter imaging technique in different microscopy platforms including conventional wide-field, dark-field, and confocal. In different platforms, we conducted label-free imaging of cells undergoing biological processes such as nanoparticle uptake, apoptosis, and metabolic flux change in response to the variation of the osmotic pressure. Hyperspectral image analyses resolved spectral endmembers corresponding to unique scattering and absorption characteristics as a result of such processes at the single particle, single organelle, and single cell level, delineating the details of nanomaterial-cell interactions in a 2D cell culture, cell apoptotic characteristics in a 3D culture, and volumetric changes of single cells under the variation of osmotic pressure. Our label-free scatter imaging has the potential for a broad range of biological and biomedical applications such as the development of scatter-based imaging contrast agents and the measurement of scatter parameters of subcellular organelles to identify the sub-micron scale origins of scattering signals in tissue scattering measurements.
A high performance inverted organic solar cell with a low band gap small molecule (p-DTS(FBTTh2)2) using a fullerene derivative-doped zinc oxide nano-film modified with a fullerene-based self-assembled monolayer as the cathode (2015)

A device with a ZnO–C60 nanofilm and NPC70-OH as a SAM gives a PCE of up to 9.14%.
Identification of compounds responsible for the odorant properties of aromatic caramel (2012)

ABSTRACT Aromatic caramel results from the heat treatment of sugars under specific temperature conditions. Because of its richness in aroma compounds and its pleasant organoleptic properties, caramel is widely used in the food industry. However, the composition of the volatile odorant fraction has not been completely elucidated. The aim of this work was thus to identify the volatile odorant compounds responsible for caramel sensory properties using a multivariate statistical technique. Four aromatic caramels differing in terms of their carbohydrate composition and cooking process were chosen. Odorant compounds were screened by gas chromatography–olfactometry (GC‐O) and identified by GC–mass spectrometry (GC‐MS). GC‐O data were processed using a detection frequency method. A total of 76 odorant zones were detected and 49 aroma compounds identified, some of them being reported for the first time in caramel. In parallel, descriptive sensory profiles of the caramels were performed with a panel of ten trained assessors. Odour properties appeared to be closely related to the cooking properties of the caramel. The relationship between the intensities of sensory descriptors and the 76 odorant zones was modelled by partial least squares regression (PLS‐R). The first PLS‐R component explained 93% of the variance in sensory descriptors and 39% in GC‐O data. Sensory descriptors were mainly separated on the first axis, opposing sweet‐like descriptors (cooked‐syrup, fruity, honey) to burnt sugar descriptors (strong, pungent, roasted). Heterocycles, carbocyclic compounds and acids appeared to be the principal odorants for burnt sugars. They were mainly described by empyreumatic notes in GC‐O and correlated to burnt sugar descriptors in the PLS model. Copyright © 2012 John Wiley &amp; Sons, Ltd.
Surface-Initiated Enzymatic Polymerization of DNA (2007)

We describe a technique to synthesize DNA homopolymers on a surface using surface-initiated enzymatic polymerization (SIEP) with terminal deoxynucleotidyl transferase (TdTase), an enzyme that repetitively adds mononucleotides to the 3'-end of oligonucleotides. The thickness of the synthesized DNA layer was found to depend on the deoxymononucleotide monomer, in the order of dATP > dTTP > dGTP approximately dCTP. In addition, the composition and the surface density of oligonucleotide initiators were also important in controlling the extent of DNA polymerization. The extension of single-stranded DNA chains by SIEP was further verified by their binding to antibodies specific to oligonucleotides. TdTase-mediated SIEP can also be used to grow spatially defined three-dimensional DNA structures by soft lithography and is a new tool for bioinspired fabrication at the micro- and nanoscale.
Revitalizing low-income public housing through community participation in the UK (1996)

Poverty is at the root of the problems facing many public housing projects in the U.K. today. Experience emerging from 100 low-income housing estates echoes findings from urban upgrading for the poor in developing countries. Tackling poverty and unemployment in low income communities cannot be left to the market alone. Community participation and full partnership with communities is key, but this is constrained by the push to achieve results quickly, as well as lack of agency interest and skills in working with poor communities as partners. Lasting change requires a strong national and regional policy framework, a new approach based on inter-agency cooperation, local delivery, and meaningful participation by local residents. Residents of such projects offer a significant resource for regeneration, particularly when they have established a foundation of local activity and organizational experience.
Embryonic and aglomerular kidney development in the bay pipefish, Syngnathus leptorhynchus (2022)

In this report we describe the embryogenesis of the bay pipefish, Syngnathus leptorhynchus, and the organogenesis of its aglomerular kidney. Early development was analyzed via a series of montages and images documenting embryos collected from the brood pouches of pregnant males. Despite differences in terminal morphology between pipefish and common teleost models such as medaka and zebrafish, the embryogenesis of these highly advanced fishes is generally similar to that of other fishes. One of the unique features of these fishes is their utilization of an aglomerular kidney. Histological analysis revealed a single long, unbranched kidney tubule in late embryos. The development and structure of this organ was further investigated by cloning the sodium potassium ATPase alpha subunit, atp1a, from S. leptorhynchus and developing whole mount fluorescent in situ hybridization protocols for embryos of this species. Fluorescent stereoscopic and confocal visualization techniques were then used to characterize the 3D morphology of aglomerular kidneys in intact embryos. In all embryonic stages characterized, the aglomerular kidney is a single unbranched tube extending from just behind the head to the cloaca.
Physical symptoms in premenstrual syndrome are related to plasma progesterone and desoxycorticosterone (2000)

Somatic symptoms in the premenstrual syndrome (PMS) may have an etiology separate from that of the mental symptoms. A disturbance in mineralocorticoid action has been discussed, as mineralocorticoids regulate water balance. Desoxycorticosterone (DOC) is interesting, as it has mineralocorticoid effects and is a precursor to the neurosteroid 5 alpha-pregnan-3 alpha,21-diol-20-one (THDOC). THDOC is a steroid with direct benzodiazepine-like effects on the GABA-A receptor in the brain that is metabolized from DOC within the brain and in the periphery. Ten women with PMS having swelling as a major symptom and eight controls were recruited. They marked, on a validated visual-analog scale, three physical symptoms every evening during one menstrual cycle in conjunction with giving blood samples for progesterone and DOC measurements. DOC showed menstrual cycle-linked variation correlating with progesterone. There was no difference in plasma DOC concentrations between patients and controls. The symptoms reached a maximum 1-3 days before the onset of menstruation, with a delay of 3-6 days after the hormone peak. DOC was less strongly correlated with the symptoms than progesterone. These results do not support the hypothesis that DOC is involved in the etiology of physical symptoms in PMS or that physical and mental symptoms have separate etiologies.
PhenDV, a turn-off fluorescent quadruplex DNA probe for improving the sensitivity of drug screening assays (2017)

We report a new turn-off fluorescent probe, PhenDV, for the identification of high affinity quadruplex (G4) DNA ligands. This push-pull fluorophore displays a high fluorescence quantum yield in water (Φ<sub>F</sub> = 0.21) and is a selective and strong quadruplex DNA binder. We describe its use as a fluorescent indicator for the G4 Fluorescent Intercalator Displacement (FID) assay as its fluorescence is strongly quenched when bound to G4 DNA and fully restored when displaced by ligand. This probe improves the sensitivity of the G4-FID assay, as the read out relies on increased fluorescence instead of quenching observed with classical on/off probes.