gebhart/patrepeval huggingface dataset:
Characterization of cocoa liquors by GC–MS and LC–MS/MS: focus on alkylpyrazines and flavanols (2012)

Flavor is one of the most important characteristics of chocolate products and is due to a complex volatile fraction, depending both on the cocoa bean genotype and the several processes occurring during chocolate production (fermentation, drying, roasting and conching). Alkylpyrazines are among the most studied volatiles, being one of the main classes of odorant compounds in cocoa products. In this work, a mass spectrometric approach was used for the comparison of cocoa liquors from different countries. A headspace solid-phase microextraction gas chromatography-mass spectrometry method was developed for the qualitative study of the volatile fraction; the standard addition method was then used for the quantitative determination of five pyrazines (2-methylpyrazine, 2,3-dimethylpyrazine, 2,5-dimethylpyrazine, 2,3,5-trimethylpyrazine and tetramethylpyrazine). Satisfactory figures of merit were obtained: Limits of quantitation were in the range 0.1-2.7 ng/g; repeatability and reproducibility varied between 3% and 7% and between 8% and 14%, respectively. The total content of the pyrazines was remarkably different in the considered samples, ranging from 99 to 708 ng/g. Tetramethylpyrazine showed the highest concentration in all samples, with a maximum value of 585 ng/g. A preliminary study was also performed on the nonvolatile fraction using LC-MS/MS, identifying some flavanols such as catechin, epicatechin and procyanidins.
Generating prospective scenarios of use in innovation projects (2014)

L’ergonomie prospective est une modalité d’intervention ergonomique centrée sur l’anticipation des besoins et activités futurs, visant à assister les premières étapes du processus de conception innovante centrée utilisateurs. À ce jour, peu de propositions méthodologiques ont été formulées pour assister les interventions en ergonomie prospective, bien que ceci constitue un levier majeur pour une meilleure intégration de la conception centrée utilisateurs dans les projets d’innovation. Ainsi, les méthodes classiques de l’analyse des usages sont d’un intérêt limité lorsque le concepteur doit travailler avec des concepts de produit mal définis, car il peut s’avérer difficile de décrire les usages futurs du produit en question. Dans cet article, nous proposons que certaines méthodes de créativité, souvent utilisées pour résoudre des problèmes de nature technique dans le cadre de projets de conception, puissent être utilisées pour élaborer des scénarios spéculatifs portant sur l’usage futur d’un produit. Nous avons réalisé des simulations de réunions de conception portant sur l’anticipation des usages de différents produits et avons évalué, au travers de deux études, les effets de méthodes empruntées à deux paradigmes de créativité sur la capacité d’une équipe pluridisciplinaire de conception à formuler des scénarios d’usage futurs. La première étude visait à évaluer les apports de méthodes empruntées au paradigme du Creative Problem Solving (CPS) – le brainwriting et la matrice de découvertes – à la production de scénarios prospectifs d’usages. Elle fait suite à une étude qui montrait que ces méthodes n’avaient pas d’effet sur le nombre de scénarios produits ni sur le nombre d’idées relatives aux usagers futurs du produit ou à leurs activités. Nous montrons ici, cependant, que ces méthodes permettent de mieux structurer la dynamique d’exploration de l’espace créatif, et d’aboutir à des idées plus originales. Dans la seconde étude, nous avons examiné la capacité d’une équipe de concepteurs à exploiter l’analyse multi-écrans – une méthode empruntée à la théorie de résolution des problèmes inventifs (TRIZ) – pour construire un discours sur les usages futurs d’un produit innovant. Les résultats suggèrent que l’équipe était en mesure d’anticiper des évolutions de l’artefact technique – ce qui correspond à la finalité initiale de la méthode – mais pas de se réapproprier l’outil pour imaginer des scénarios illustrant les usages futurs possibles du produit. Nous décrivons enfin les conséquences de ces résultats pour élaborer de nouvelles méthodologies d’intervention en ergonomie prospective.
Theory of Block Copolymer Self-assembly Lithographic Imaging Mechanisms (2016)

Lithography based on self-assembling block copolymers exploits the phase separation of block copolymer domains into nanoscopic structures that can be used as lithographic masks—templates for patterning and synthesizing inorganic materials and printing biomaterials. But before we proceed further, it is necessary to provide a brief background on block copolymers, how they are made, the condition under which they phase separate and self-assemble, and why they do this. Block copolymers (BCPs) comprise two or more chemically distinct polymer chains (called blocks) that are covalently bonded at one end to form a larger, more complex macromolecule. If the constituent polymers are immiscible, upon heating, phase separation can be induced (without resulting in total separation because of the covalent bonding connectivity between the copolymer chains). The separated phases are on a scale that is directly related to the size of the copolymer chains, resulting in morphologies typified by a pattern of chemically distinct domains of periodicity L0 in the 5- to 100-nm range. The size, shape, and arrangement of these morphologies are all tunable through synthetic chemistry of the constituent molecules, thereby enabling a diverse and expanding range of practical applications in, for example, drug delivery, lithographic masks, photonic and electronic materials, and advanced plastics, to mention but a few. Buoyed by new developments, block copolymers, thoroughly studied for more than 50 years, are yet again garnering renewed research interest, principally because of their potential applications in nanotechnology, of which lithography is an enabler.
Announcement:  New Associate Editor (2005)

ADVERTISEMENT RETURN TO ISSUEEditorialNEXTAnnouncement: New Associate EditorDonald R. PaulView Author Information Department of Chemical Engineering University of Texas at Austin Austin, Texas 78712-0231Cite this: Ind. Eng. Chem. Res. 2006, 45, 2, 481Publication Date (Web):December 21, 2005Publication History Published online21 December 2005Published inissue 1 January 2006https://pubs.acs.org/doi/10.1021/ie0513696https://doi.org/10.1021/ie0513696editorialACS PublicationsCopyright © 2006 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views256Altmetric-Citations-LEARN 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 InRedditEmail PDF (5 KB) Get e-Alertsclose Get e-Alerts
SU‐E‐J‐138: On the Ion Beam Range and Dose Verification in Hadron Therapy Using Sound Waves (2015)

Purpose: Accurate range verification is of great importance to fully exploit the potential benefits of ion beam therapies. Current research efforts on this topic include the use of PET imaging of induced activity, detection of emerging prompt gamma rays or secondary particles. It has also been suggested recently to detect the ultrasound waves emitted through the ion energy absorption process. The energy absorbed in a medium is dissipated as heat, followed by thermal expansion that leads to generation of acoustic waves. By using an array of ultrasound transducers the precise spatial location of the Bragg peak can be obtained. The shape and intensity of the emitted ultrasound pulse depend on several variables including the absorbed energy and the pulse length. The main objective of this work is to understand how the ultrasound wave amplitude and shape depend on the initial ion energy and intensity. This would help guide future experiments in ionoacoustic imaging. Methods: The absorbed energy density for protons and carbon ions of different energy and field sizes were obtained using Fluka Monte Carlo code. Subsequently, the system of coupled equations for temperature and pressure is solved for different ion pulse intensities and lengths to obtain the pressure wave shape, amplitude and spectral distribution. Results: The proposed calculations show that the excited pressure wave amplitude is proportional to the absorbed energy density and for longer ion pulses inversely proportional to the ion pulse duration. It is also shown that the resulting ionoacoustic pressure distribution depends on both ion pulse duration and time between the pulses. Conclusion: The Bragg peak localization using ionoacoustic signal may eventually lead to the development of an alternative imaging method with sub‐millimeter resolution. It may also open a way for in‐vivo dose verification from the measured acoustic signal.
Manifestation of coherent effects in the conductivity of superconductor/insulator/normal-metal/insulator/superconductor junctions (2003)

An experimental and theoretical study is presented of coherent effects in electron transport in the double-barrier SINIS junctions (where S, I, and N denote a superconductor, insulator, and normal metal, respectively). The appearance of a steplike subgap structure in the current-voltage characteristics of the $\mathrm{Nb}/\mathrm{Al}/{\mathrm{AlO}}_{x}/\mathrm{Al}/{\mathrm{AlO}}_{x}/\mathrm{Al}/\mathrm{Nb}$ superconducting junctions at a voltage $V\ensuremath{\sim}{\ensuremath{\Delta}}_{\mathrm{Nb}}/e$ (where ${\ensuremath{\Delta}}_{\mathrm{Nb}}$ is the superconducting energy gap of Nb) is interpreted as a manifestation of a nonequilibrium supercurrent at finite dc bias voltage (Finite-Bias Josephson Effect). The origin of this effect lies in the energy-band structure associated with a set of macroscopic quantum states characteristic of a SINIS junction. Specifically, the junction can have an energy level near energy ${\ensuremath{\Delta}}_{\mathrm{Nb}},$ which provides an additional channel for dc Josephson current at $V\ensuremath{\sim}{\ensuremath{\Delta}}_{\mathrm{Nb}}/e.$ In addition, sharp features in the conductivity at a voltage near the gap-sum voltage were observed in both SINIS and SINININIS junctions, implying correlated quasiparticle tunneling in multiple-barrier junctions. Our theoretical model provides a good qualitative description of the quasiparticle conductivity, including narrow peaks at finite voltage and a zero-voltage anomaly observed on some samples, and suggests an alternative explanation of a feature interpreted earlier as gap-difference feature associated with the tunneling extraction of quasiparticles from the middle Al layer.
New Partners Identified by Mass Spectrometry Assay Reveal Functions of NCAM2 in Neural Cytoskeleton Organization (2021)

Neuronal cell adhesion molecule 2 (NCAM2) is a membrane protein with an important role in the morphological development of neurons. In the cortex and the hippocampus, NCAM2 is essential for proper neuronal differentiation, dendritic and axonal outgrowth and synapse formation. However, little is known about NCAM2 functional mechanisms and its interactive partners during brain development. Here we used mass spectrometry to study the molecular interactome of NCAM2 in the second postnatal week of the mouse cerebral cortex. We found that NCAM2 interacts with >100 proteins involved in numerous processes, including neuronal morphogenesis and synaptogenesis. We validated the most relevant interactors, including Neurofilaments (NEFs), Microtubule-associated protein 2 (MAP2), Calcium/calmodulin kinase II alpha (CaMKIIα), Actin and Nogo. An in silico analysis of the cytosolic tail of the NCAM2.1 isoform revealed specific phosphorylation site motifs with a putative affinity for some of these interactors. Our results expand the knowledge of NCAM2 interactome and confirm the key role of NCAM2 in cytoskeleton organization, neuronal morphogenesis and synaptogenesis. These findings are of interest in explaining the phenotypes observed in different pathologies with alterations in the NCAM2 gene.
Phase I Trial of EC90 (keyhole-limpet hemocyanin fluorescein isothiocyanate conjugate) with GPI-0100 adjuvant followed by EC 17 (folate-fluorescein isothiocyanate conjugate) in patients with metastatic renal cell carcinoma and ovarian cancer (2004)

4754 Background: FolateImmune is a novel immunotherapy comprised of a vaccine EC90 with GP-0100 adjuvant and a folate-conjugated vaccine( EC-17) that targets folate receptor (FR) positive tumor cells to enhance tumor cell removal by cytokine stimulated immune cells. The over-expression of the FR occurs in a number of malignancies, including kidney, & ovarian. Methods: FolateImmune treatment begins with a series of subcutaneous inoculations of EC90 (0.2mg/dose), a KLH-FITC conjugate adjuvanted with GP-0100 (3.0mg/dose) to stimulate the production of antibodies to FITC. The patient then receives a subcutaneous injection of EC17, a folate FITC conjugate, that binds to cells over-expressing the FR and promotes their opsonization with the previously induced endogenous anti-FITC IgG. This process effectively marks the tumor cells for subsequent immune recognition. EC17 forms a molecular bridge between the tumor cell and the endogenous circulating anti-FITC IgG. This marking initiates an Fc-mediated immune response leading to the removal of the antibody-coated tumor cells. Eligibility included positive immunohistochemical confirmation of folate receptors on tumor tissue, ECOG score of ≤ 1, life expectancy >3 months, any prior chemotherapy or immunotherapy, normal organ/marrow function, measurable disease, and no active CNS disease. Results: 6 patients have been enrolled in dose level 0 of EC 17 (0.031mg/kg). 5 patients had RCC (4 patients clear cell, 1 patients papillary) and 1 patient had ovarian carcinoma. All patients had one or more prior treatments. No toxicities were seen at dose level 0. 6 RCC patients are preparing to begin dose level plus 1 (0.92mg/kg) 3 of the renal cell patients by RECIST criteria are stable and beginning a second cycle of therapy. No significant toxicity has been observed. Laboratory correlates are presently being analyzed. Conclusions: FolateImmune therapy is well tolerated with a suggestion of biologic activity reflected in that three patients are continuing therapy. Additional results will be updated at the meeting. Author Disclosure Employment or Leadership Consultant or Advisory Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Endocyte
Pose Classification using 3D Atomic Structure-Based Neural Networks Applied to Ion Channel-Ligand Docking (2022)

The identification of promising lead compounds showing pharmacological activities toward a biological target is essential in early-stage drug discovery. With the recent increase in available small–molecule databases, virtual high-throughput screening using physics-based molecular docking has emerged as an essential tool in assisting fast and cost-efficient lead discovery and optimization. However, the best scored docking poses are often suboptimal, resulting in incorrect screening and chemical property calculation. We address the pose classification problem by leveraging data-driven machine learning approaches to identify correct docking poses from AutoDock Vina and Glide screens. To enable effective classification of docking poses, we present two convolutional neural network approaches: a 3D convolutional neural network (3D-CNN) and an attention-based point cloud network (PCN) trained on the PDBbind refined set. We demonstrate the effectiveness of our proposed classifiers on multiple evaluation datasets including the standard PDBbind CASF-2016 benchmark dataset and various compound libraries with structurally different protein targets including an ion-channel dataset extracted from Protein Data Bank (PDB) and an inhouse KCa3.1 inhibitor dataset. Our experiments show that excluding false-positive docking poses using the proposed classifiers improves virtual high-throughput screening to identify novel molecules against each target protein, compared to the initial screen based on the docking scores.
Identification of Domains Participating in the Substrate Specificity and Subcellular Localization of the Multidrug Resistance Proteins MRP1 and MRP2 (2003)

The human multidrug resistance protein MRP1 and its homolog, MRP2, are both thought to be involved in cancer drug resistance and the transport of a wide variety of organic anions, including the cysteinyl leukotriene C4 (LTC4) (Km = 0.1 and 1 microm). To determine which domain of these proteins is associated with substrate specificity and subcellular localization, we constructed various chimeric MRP1/MRP2 molecules and expressed them in polarized mammalian LLC-PK1 cells. We examined the kinetic properties of each chimeric protein by measuring LTC4 and methotrexate transport in inside-out membrane vesicles, sensitivity to an anticancer agent, etoposide, and subcellular localization by indirect immunofluorescence methods. The following results were determined in these studies: (i) when the NH2-proximal 108 amino acids of MRP2, including transmembrane (TM) helices 1-3, were exchanged with the corresponding region of MRP1, Km(LTC4) values of the chimera decreased approximately 4-fold and Km(methotrexate) values increased approximately 5-fold relative to those of wild-type MRP2 and MRP1, respectively, whereas resistance to etoposide increased approximately 3-fold; (ii) when the NH2-proximal region up to TM9 of MRP2 was exchanged with the corresponding region of MRP1, a further increase in etoposide resistance was observed, and subcellular localization moved from the apical to the lateral membrane; (iii) when two-thirds of MRP2 at the NH2 terminus were exchanged with the corresponding MRP1 region, the chimeric protein transported LTC4 with an efficiency comparable with that achieved by the wild-type MRP1; and (iv) exchange of the COOH-terminal 51 amino acids between MRP1 and MRP2 did not affect the localization of either of the proteins. These results provide a strong framework for further studies aimed at determining the precise domains of MRP1 and MRP2 with affinity for LTC4 and anticancer agents.
Method for measuring small optical absorption coefficients with use of a Shack-Hartmann wave-front detector (2003)

We present a method for measuring absorption at the 1 x 10(-5) cm(-1) level in high-quality optical materials. Using a Shack-Hartmann wave-front detector, thermal lensing in these materials may be measured. Then, the absorption coefficient may be estimated by fitting the observed deformation to a thermal lensing model based on the temperature dependences of the refractive index and the thermal expansion coefficient. For a particular sample of fused silica, the absorption coefficient was determined to be 1.8 +/- 0.4 x 10(-5) cm(-1). Obtaining this result requires a resolution in the optical path length better than +/- 0.1 nm.
ChemInform Abstract: METATHESIS OF ACETYLENES BY (FLUOROALKOXY)TUNGSTENACYCLOBUTADIENE COMPLEXES AND THE CRYSTAL STRUCTURE OF W(C3ET3)(OCH(CF3)2)3. A HIGHER ORDER MECHANISM FOR ACETYLENE METATHESIS (1985)

Abstract Die Reaktion von 3 Äquiv. der Li‐alkoxide (II) bzw. (IV) mit dem W‐Komplex (I) liefert die Produkte (III) bzw. (V).
Trends in Head Injury Incidence in New Zealand: A Hospital-Based Study from 1997/1998 to 2003/2004 (2008)

Traumatic brain injury (TBI) is a leading cause of disability and death in young adults. Globally, the incidence of TBI hospitalizations is estimated at 200-300 people per 100,000 annually. Using a national health database, we examined the incidence of TBI-related hospital discharges (including 1-day stays) to New Zealand Hospitals from 1997/1998 to 2003/2004. Crude annual hospital-based incidence rates for the total population ranged from 226.9 per 100,000 in 1998/1999 to a high rate of 349.2 in 2002/2003. There was a noticeable increase in rates with the change from ICD-9 to ICD-10 diagnostic codes and there was also disparity in incidence rates according to ethnicity, age and gender. Crude annual hospital-based incidence rates for males and females in Maori (689/100,000 and 302.8/100,000 person-years) and Pacific Island populations (582.6/100,000 and 217.6/100,000 person-years) were much higher than those for the remaining population (435.4/100,000 and 200.9/100,000 person-years), particularly for males. The overall age-standardized hospital- based incidence rate for 2003/2004 was 342 per 100,000 per year (95% CI = 337-349/100,000), and 458 per 100,000 per year for Maori (95% CI = 438-479/100,000) with Maori males experiencing a peak in incidence between 30 and 34 years of age that was not evidenced for the wider population. Standardized hospital-based incidence rates for the total population and for Maori by age, gender and ICD-10 diagnostic codes are also examined.
The effect of different mitral annuloplasty rings on valve geometry and annular stress distribution† (2017)

This study is the first to describe different remodelling effects and deformational forces of normosized mitral annuloplasty rings in vivo . Insights into the relationship between the remodelling effects and the accumulated forces of different mitral annuloplasty rings may have implications for ring selections in an aetiology-based mitral valve repair strategy. We propose the application of such a biomechanical approach for quantitative comparison of mitral annuloplasty rings and for future innovations on a rational basis.
Modelling Pronominal Anaphora in Statistical Machine Translation (2010)

Current Statistical Machine Translation (SMT) systems translate texts sentence by sentence without considering any cross-sentential context. Assuming independence between sentences makes it difficult to take certain translation decisions when the necessary information cannot be determined locally. We argue for the necessity to include cross-sentence dependencies in SMT. As a case in point, we study the problem of pronominal anaphora translation by manually evaluating German-English SMT output. We then present a word dependency model for SMT, which can represent links between word pairs in the same or in different sentences. We use this model to integrate the output of a coreference resolution system into English-German SMT with a view to improving the translation of anaphoric pronouns.
Effect of intraocular lens design on migration of lens epithelial cells onto the posterior capsule (1997)

In the rabbit-model study, the convex-plano lens was superior to the biconvex lens in inhibiting migration of LECs. A firm contact between the IOL and the posterior capsule blocked the migration.