gebhart/patrepeval huggingface dataset:
Fecal Gluten Peptides Reveal Limitations of Serological Tests and Food Questionnaires for Monitoring Gluten-Free Diet in Celiac Disease Patients (2016)

Detection of gluten peptides in stools reveals limitations of traditional methods for monitoring GFD in celiac patients. The GIP ELISA enables direct and quantitative assessment of gluten exposure early after ingestion and could aid in the diagnosis and clinical management of nonresponsive CD and refractory CD. Trial registration number NCT02711397.
Helical cone beam reconstruction in volumetric CT: maintaining a large field-of-view (FOV) at very high pitches (2005)

In volumetric CT, the suppression of cone beam (CB) and helical artifacts is very challenging. At very high pitches larger than 1.5, not only artifact suppression but also maintenance of a large field of view (FOV) become even more challenging. At large helical pitches, the data redundancy corresponding to each pixel within a reconstruction FOV varies dramatically. An inappropriate dealing with the fast-varying data redundancy over pixels to be reconstructed can result in severe shading/glaring artifacts in reconstructed images and lead a clinical diagnosis impossible. One existing approach to combat the non-uniform data redundancy and extend the FOV at very high pitches is to reconstruct images on tilted planes. However, tilting a reconstruction plane can significantly impacts data flow of filtered backprojection -- the most attractive one practiced by all major CT manufacturers -- and slows down image generation speed considerably. Along with an experimental evaluation, a helical CB filtered backprojection reconstruction algorithm using three-dimensional view weighting (namely 3D view weighted CB-FBP algorithm) is proposed here. The novelty of the proposed algorithm is the 3D-nature of the weighting function, which enables the proposed algorithm to reach the optimal image qualities and provides the freedom in controlling image quality over accuracy, noise characteristics, spatial resolution and temporal resolution. Particularly, it is the 3D view weighting that enables the proposed algorithm to maintain an FOV at helical pitch larger than 1.5, which is as large as that at helical pitches below 1.0. It is believed that the proposed 3D view weighted CB-FBP algorithm is applicable to and robust over all CT imaging applications, including diagnostic imaging and dynamic imaging for functional evaluation. It is also believed that the proposed algorithm will work well for larger cone angles when more sophisticated 3D view weighting strategies are employed.
Total Synthesis of Anthracyclinone [New Synthetic Methods (60)] (1986)

Abstract The remarkable antitumor properties of anthracycline antibiotics have motivated synthetic chemists, and a large number of groups have been active recently in this field. Initially, there was very little hope for this class of substances due to their extreme toxicity. However, the dividing line between toxicity and desired pharmacological effect has broadened to such an extent, partly through microbiological methods (new strains, mutants) and partly through semisynthetic modifications, that today anthracyclines take number one place (over 20% of the market) in the chemotherapy of (human) cancer. The demands made on modern cytostatica are extremely high, as may be seen from the fact that of the more than 600000 drugs tested in animals, only about 40 are in clinical use. In the meantime, some anthracyclines obtained by total synthesis are also in clinical testing. In this review it will hopefully be demonstrated that all those concerned in the chemotherapeutic use of these substances have also contributed to the general progress made in the solution of regio‐ and stereo‐chemical problems of linearly annelated ring systems.
Comparison of static and agitated immobilized cultures of <i>Phanerochaete chrysosporium</i> for the degradation of pentachlorophenol and its metabolite pentachloroanisole (1997)

The transformation of pentachlorophenol (PCP) by Phanerochaete chrysosporium I-1512 in relation to pentachloroanisole (PCA) was studied in two different modes of culture. The degradation of PCP by immobilized cells in agitated medium was compared with that by static cultures. Results clearly established the advantage of an immobilized culture for mineralization of PCP: 23% of CO 2 released for fungus immobilized on stainless steel mesh rings as compared with 11% for static cultures. PCA, a metabolite of PCP, was formed only in static cultures and underwent a limited mineralization. Moreover, experiments performed with mycelium and culture supernatant (in the presence of cycloheximide) clearly demonstrated that PCA formation was catalyzed by the biomass in static cultures of P. chrysosporium. Assays in vitro did not establish any involvement of lignin or manganese peroxidases in PCP or PCA transformation.Key words: filamentous fungi, Phanerochaete chrysosporium, pentachlorophenol, pentachloroanisole.
High efficiency collision-induced dissociation in an rf-only quadrupole. Interim technical report. [5 to 10 eV] (1978)

Collision-induced dissociation (CID), when performed in an RF-only quadrupole is a highly efficient method of fragmenting ions. The low-energy (5-10 eV) CID process, may involve direct vibrational excitation by momentum transfer but in any case, is a very different process from the high energy (3-10 keV) electronic excitation CID process observed in MIKES and CAMS. Experimental results are presented which demonstrate the efficiency of CID fragmentation (up to 65%), the elimination of scattering losses, and the effects of varying such experimental parameters as choice and pressure of collision gas, ion velocity in the quadrupole, and quadrupole RF voltage and frequency. The appearance of the CID fragmentation spectra is roughly similar to 14 eV EI spectra. The results of digital simulation of ion trajectories in an RF-only quadrupole are presented. The correspondence between simulated and experimental results aids in the understanding of the quadrupole CID process. The high efficiency of the CID process in an RF-only quadrupole is significant in the development of a tandem quadrupole mass spectrometer for selected ion fragmentation studies.
Generation of Ti<sup>II</sup> Alkyne Trimerization Catalysts in the Absence of Strong Metal Reductants (2017)

Low-valent Ti<sup>II</sup> species have typically been synthesized by the reaction of Ti<sup>IV</sup> halides with strong metal reductants. Herein we report that Ti<sup>II</sup> species can be generated simply by reacting Ti<sup>IV</sup> imido complexes with 2 equiv of alkyne, yielding a metallacycle that can reductively eliminate pyrrole while liberating Ti<sup>II</sup>. In order to probe the generality of this process, Ti<sup>II</sup>-catalyzed alkyne trimerization reactions were carried out with a diverse range of Ti<sup>IV</sup> precatalysts.
Water-in-Water Emulsions Stabilized by Non-Amphiphilic Interactions:  Polymer-Dispersed Lyotropic Liquid Crystals (2006)

Emulsion systems involving surfactants are mainly driven by the separation of the hydrophobic interactions of the aliphatic chains from the hydrophilic interactions of amphiphilic molecules in water. In this study, we report an emulsion system that does not include amphiphilic molecules but molecules with functional groups that are completely solvated in water. These functional groups give rise to molecular interactions including hydrogen bonding, pi stacking, and salt bridging and are segregated into a dispersion of droplets forming a water-in-water emulsion. This water-in-water emulsion consists of dispersing droplets of a water-solvated biocompatible liquid crystal--disodium cromoglycate (DSCG)--in a continuous aqueous solution containing specific classes of water-soluble polymers. Whereas aqueous solutions of polyols support the formation of emulsions of spherical droplets consisting of lyotropic liquid crystal DSCG with long-term stability (for at least 30 days), aqueous solutions of polyamides afford droplets of DSCG in the shape of prolate ellipsoids that are stable for only 2 days. The DSCG liquid crystal in spherical droplets assumes a radial configuration in which the optical axis of the liquid crystal aligns perpendicular to the surface of the droplets but assumes a tangential configuration in prolate ellipsoids in which the optical axis of the liquid crystal aligns parallel to the surface of the droplet. Other classes of water-soluble polymers including polyethers, polycations, and polyanions do not afford a stable emulsion of DSCG droplets. Both the occurrence and the stability of this unique emulsion system can be rationalized on the basis of the functional groups of the polymer. The different configurations of the liquid crystal (DSCG) droplets were also found to correlate with the strength of the hydrogen bonding that can be formed by the functional groups on the polymer.
Formation domain of SDA-free Y faujasite small crystals (2017)

The ternary phase diagram shows that the domain for obtaining Y faujasite small crystals is very narrow.
<i>Apolipoprotein A5</i> , a Newly Identified Gene That Affects Plasma Triglyceride Levels in Humans and Mice (2003)

Apolipoprotein A5 (APOA5) is a newly described member of the apolipoprotein gene family whose initial discovery arose from comparative sequence analysis of the mammalian APOA1/C3/A4 gene cluster. Functional studies in mice indicated that alteration in the level of APOA5 significantly affected plasma triglyceride concentrations. Mice that overexpressed human APOA5 displayed significantly reduced triglycerides, whereas mice that lacked apoa5 had a large increase in this lipid parameter. Studies in humans have also suggested an important role for APOA5 in determining plasma triglyceride concentrations. In these experiments, polymorphisms in the human gene were found to define several common haplotypes that were associated with significant changes in triglyceride concentrations in multiple populations. Several separate clinical studies have provided consistent and strong support for the effect with 24% of whites, 35% of blacks, and 53% of Hispanics who carry APOA5 haplotypes associated with increased plasma triglyceride levels. In summary, APOA5 represents a newly discovered gene involved in triglyceride metabolism in both humans and mice whose mechanism of action remains to be deciphered.
Design and Enantioselective Synthesis of a Peptidomimetic of the Turn in the Helix−Turn−Helix DNA-Binding Protein Motif (1997)

A peptidomimetic of the turn in the helix-turn-helix (HTH) motif of DNA-binding proteins was designed and synthesized. Conformational constraint was achieved by an unusual linking of two amino acids with a side chain carbon-carbon bond. A phenyl ring provides the potential for new hydrophobic contacts with the hydrophobic core of the HTH motif. In the mimic, the peptide backbone and the central residue were retained in native form within a 12-membered cyclic tripeptide. The target compound 1b was synthesized by two sequential Horner-Wittig couplings followed by enantioselective hydrogenation with Rh(MeDuPHOS) in eight steps and 35% overall yield. The stereochemical outcome of the key hydrogenation was determined by aromatic ring oxidation with RuO(2)/NaIO(4) to give 2 equiv of Boc-Asp-OMe.
Increased internal noise cannot account for motion coherence processing deficits in migraine (2011)

The results from this study suggest that variation in internal noise levels is not the mechanism driving motion coherence threshold differences in migraine. Rather, we argue that motion processing deficits may result from cortical changes leading to less efficient extraction of global-motion signals from noise.
Power efficient system for sensor networks (2004)

We propose a power efficient system architecture that exploits the characteristics of sensor networks in order to decrease the power consumption in the network. The primary characteristic of sensor networks is that the destination of all the data packets in the network is a central data collector, which is usually denoted as access point (AP), has unlimited transmission power and energy whereas the sensor nodes have one battery energy to remain alive fro several years. Our system uses the AP to directly synchronize and explicitly schedule the nodes' transmissions over time division multiple access (TDMA) time slots. Simulations performed in TOSSIM, a simulation environment for the TinyOS, show that the battery lifetime of the network with this scheme can be increased to 1-2 years from 10 days that can be obtained from a general random access network.
Purification and characterization of a phosphatidylinositol 4-kinase from bovine uteri. (1988)

Phosphatidylinositol 4-kinase has been purified 10,148-fold to a specific activity of 2.7 mumol/mg/min from bovine uteri. This purification was accomplished by detergent extraction of an acetone powder, ammonium sulfate precipitation, and chromatography on MonoQ, S-Sepharose, MonoP, and hydroxylapatite columns. The purified enzyme has a molecular mass of 55 kDa and appears to be monomeric. Kinetic analyses of the enzymatic activity demonstrated apparent Km values of 18 microM and 22 micrograms/ml (approximately 26 microM) for ATP and phosphatidylinositol, respectively, optimal activity in the pH range of 6.0-7.0, and a sigmoidal dependence of enzymatic activity on [Mg2+]. Ca2+ inhibited the enzyme at nonphysiological concentrations with 50% inhibition observed at a free [Ca2+] of approximately 300 microM. The purified enzyme efficiently utilized both ATP and 2'-deoxy-ATP as phosphoryl donors and specifically phosphorylated phosphatidylinositol on the fourth position. No phosphatidylinositol-4-phosphate 5-kinase activity was observed in the purified enzyme preparations. To our knowledge, this is the first reported purification of a phosphatidylinositol-specific phosphatidylinositol 4-kinase.
Vaccination with Ectoparasite Proteins Involved in Midgut Function and Blood Digestion Reduces Salmon Louse Infestations (2020)

Infestation with the salmon louse <i>Lepeophtheirus salmonis</i> (Copepoda, Caligidae) affects Atlantic salmon (<i>Salmo salar</i> L.) production in European aquaculture. Furthermore, high levels of salmon lice in farms significantly increase challenge pressure against wild salmon populations. Currently, available control methods for salmon louse have limitations, and vaccination appears as an attractive, environmentally sound strategy. In this study, we addressed one of the main limitations for vaccine development, the identification of candidate protective antigens. Based on recent advances in tick vaccine research, herein, we targeted the salmon louse midgut function and blood digestion for the identification of candidate target proteins for the control of ectoparasite infestations. The results of this translational approach resulted in the identification and subsequent evaluation of the new candidate protective antigens, putative Toll-like receptor 6 (P30), and potassium chloride, and amino acid transporter (P33). Vaccination with these antigens provided protection in Atlantic salmon by reducing adult female (P33) or chalimus II (P30) sea lice infestations. These results support the development of vaccines for the control of sea lice infestations.
Synthesis and Biological Evaluation of Bisindenoisoquinolines as Topoisomerase I Inhibitors (2006)

The indenoisoquinolines represent a class of non-camptothecin topoisomerase I (Top1) inhibitors that exert cytotoxicity by trapping the covalent complex formed between DNA and Top1 during relaxation of DNA supercoils. As an ongoing evaluation of Top1 inhibition and anticancer activity, indenoisoquinolines were linked via their lactam side chains to provide polyamines end-capped with intercalating motifs. The resulting bisindenoisoquinolines were evaluated for cytotoxicity in the National Cancer Institute's human cancer cell screen and for Top1 inhibition. Preliminary findings suggested that the 2-3-2 and 3-3-3 linkers, referring to the number of carbons between nitrogen atoms, were optimal for both potent Top1 inhibition and cytotoxicity. Using optimized linkers, bisindenoisoquinolines were synthesized with nitro and methoxy substituents on the aromatic rings. The biological results for substituted compounds revealed a disagreement between the structure-activity relationships of monomeric indenoisoquinolines and bisindenoisoquinolines as Top1 inhibitors, but cytotoxicity was maintained for both series of compounds.
The Sulfakinins of the Blowfly Calliphora Vomitoria. Peptide Isolation, Gene Cloning and Expression Studies (1995)

The nonapeptide, Phe-Asp-Asp-Tyr(SO3)-Gly-His-Met-Arg-Phe-NH2 was isolated from heads of the blowfly Calliphora vomitoria. Designated callisulfakinin I, the peptide is identical to the earlier known drosulfakinin I of Drosophila melanogaster and to neosulfakinin I of Neobellieria bullata. It belongs to the sulfakinin family, all known members of which (from flies, cockroaches and locusts) have the C-terminal heptapeptide sequence Asp-Tyr(SO3)-Gly-His-Met-Arg-Phe-NH2. The callisulfakinin gene of C. vomitoria was cloned and sequenced. In addition to callisulfakinin I, the DNA revealed a coding sequence for the putative tetradecapeptide, Gly-Gly-Glu-Glu-Gln-Phe-Asp-Asp-Tyr-Gly-His-Met-Arg-Phe-NH2, callisulfakinin II. However, this peptide was not identified in the fly head extracts. Confocal laser scanning immunocytochemical studies with antisera raised against the synthetic undecapeptide C-terminal fragment of drosulfakinin II from D. melanogaster, Asp-Gln-Phe-Asp-Asp-Tyr(SO3)-Gly-His-Met-Arg-Phe-NH2, revealed only four pairs of sulfakinin neurones in the brain of C. vomitoria and no others anywhere else in the neural, endocrine or gut tissues. In situ hybridisation studies with a digoxigenin-labelled sulfakinin gene probe (from the blowfly Lucilia cuprina) also revealed only four pairs of neurones in the brain. The perikarya of two pairs of cells are situated medially in the caudo-dorsal region, close to the roots of the ocellar nerve. The other perikarya are slightly more posterior and lateral. Although it has been suggested by several authors that the insect sulfakinins are homologous to the vertebrate peptides gastrin and cholecystokinin, such arguments (based essentially on C-terminal structural similarities) do not take account of important differences in the C-terminal tetrapeptide, His-Met-Arg-Phe-NH2 in the sulfakinins, compared with Trp-Met-Asp-Phe-NH2 in gastrin and cholecystokinin. Furthermore, whereas the sulfakinin neurones of C. vomitoria are small in number and have a very specialised location, a greater number of cells throughout the nervous system react positively to gastrin/cholecystokinin antisera. Chromatographic profiles of the present study also revealed peaks of gastrin/cholecystokinin-immunoreactive material separate from the sulfakinin peptides. This evidence suggests that the insect and vertebrate peptides may not necessarily be homologous.
X-ray mask repair with focused ion beams (1990)

The application of focused ion beams to the repair of defects in x-ray masks is described. An image of the defective region on the mask is obtained using the ion beam in a manner analogous to a scanning electron microscope. Opaque defects are removed by physical sputtering of extra absorber. Clear defects are repaired by ion-beam-induced decomposition of an organometallic compound to form an opaque film on the substrate. Examples illustrating the repair process and demonstrating submicron spatial resolution are presented. The effect of ion channeling on imaging and opaque repair is also described.
A Check on Rational Drug Design: Crystal Structure of a Complex of Human Immunodeficiency Virus Type 1 Protease with a Novel .gamma.-Turn Mimetic Inhibitor (1995)

We have previously reported (Newlander et al., J. Med. Chem. 1993, 36, 2321-2331) the design of human immunodeficiency virus type 1 (HIV-1) protease inhibitors incorporating C7 mimetics that lock three amino acid residues of a peptide sequence into a gamma-turn. The design of one such compound, SB203238, was based on X-ray structures of reduced amide aspartyl protease inhibitors. It incorporates a gamma-turn mimetic in the P2-P1' position, where the carbonyl of the C7 ring is replaced with an sp3 methylene group yielding a constrained reduced amide. It shows competitive inhibition with Ki = 430 nM at pH 6.0. The three-dimensional structure of SB203238 bound to the active site of HIV-1 protease has been determined at 2.3 A resolution by X-ray diffraction and refined to a crystallographic R-factor (R = sigma magnitude of Fo magnitude of - magnitude of Fc magnitude of /sigma magnitude of Fo magnitude of, where Fo and Fc are the observed and calculated structure factor amplitudes, respectively) of 0.177. The inhibitor lies in an extended conformation in the active site; however, because of the constrained geometry of the C7 ring, it maintains fewer hydrogen bonds with the protein than in most other HIV-1 protease-inhibitor complexes. More importantly, the inhibitor binds to the enzyme differently than predicted in its design, by binding with the P2-P1' alpha-carbon atoms shifted by approximately one-half a residue toward the N-terminus from their presumed positions. This study illustrates the importance of structural information in an approach to rational drug design.
A Scalable Approach to Determine Intracardiac Pressure From Mechanical Circulatory Support Device Signals (2020)

This method improves upon existing LVEDP measures without the need for rigorous characterization, external calibration, or additional intervention; this allows widescale deployment of continuous LVEDP measurement for patients on MCS and demonstrates key considerations necessary to translate research-grade technologies.