gebhart/patrepeval huggingface dataset:
Palladium-mediated biomimetic synthesis of narwedine (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPalladium-mediated biomimetic synthesis of narwedineRobert A. Holton, Mukund P. Sibi, and William S. MurphyCite this: J. Am. Chem. Soc. 1988, 110, 1, 314–316Publication Date (Print):January 1, 1988Publication History Published online1 May 2002Published inissue 1 January 1988https://pubs.acs.org/doi/10.1021/ja00209a064https://doi.org/10.1021/ja00209a064research-articleACS PublicationsRequest reuse permissionsArticle Views568Altmetric-Citations43LEARN 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 Other access optionsGet e-Alertsclose Get e-Alerts
Aperture compensated radon and fourier transforms (2009)

In seismic data analysis, recorded data often are transformed to various domains to discriminate against coherent and incoherent noise. For instance, by mapping a shot record from time-space domain to frequency-wavenumber domain, coherent linear noise can be attenuated. Similarly, by mapping a common-midpoint gather from time-space to time-velocity domain (velocity stacks) multiples are separated from primaries based on moveout discrimination. In these procedures the correct identification of seismic events with similar moveout can be severely affected by the aperture of the array and the discrete sampling of the wavefield. Economic and/or logistic reasons usually dictate the cable length and spatial sampling of the seismic experiment. This thesis examines how the resolution (the ability to distinguish close events) of slant stack and parabolic stack operators deteriorates under limited aperture. An algorithm is developed to increase the resolution of the aforementioned operators. This procedure constructs an operator that collapses each seismic signal in the transform domain, thus diminishing truncation artifacts. The overall procedure is equivalent to the simulation of a longer array of receivers. Slant stacks and the parabolic stacks are linear operations used to map the seismic data into another domain, the transform domain (r — p or r — q). In this thesis an inverse problem is posed. This is accomplished by considering the data as the result of a linear operation onto the transform domain. This approach permits one to incorporate prior information into the problem which is utilized to attenuate truncation artifacts. The prior information is incorporated into the inverse problem by means of the Bayesian formalism. The observational errors and the prior information are combined through Bayes' rule using the likelihood function and a long tailed distribution, respectively. The posteriori probability is then used to induce the objective function of the problem. Finally, minimizing the objective function leads to the solution of the inverse problem. The advantage of incorporating a long tailed distribution to model the transform domain is that the solution is constrained to be sparse which is a desired feature for highly resolved models. The method is also used to design an artifacts-reduced 2-D discrete Fourier transform. A by-product of the method is a high resolution periodogram. This periodogram coincides with the periodogram that would have been computed with a longer array of receivers if the data consist of a limited superposition of linear events.
COLD-PCR Finds Hot Application in Mutation Analysis (2009)

With the rapid development of targeted therapy and personalized medicine, gaining knowledge of the genetic and molecular characteristics of a patient’s tumor has become a crucial step in therapeutic and prognostic decision-making in oncology. A good example is the administration of therapy targeting the epidermal growth factor receptor (EGFR)1 in cancer patients. Several studies have shown that mutations that cause constitutive activation of the KRAS 2 oncogene (v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog) predict resistance to anti-EGFR therapy (1)(2)(3), whereas activating mutations in EGFR predict response to therapy and favorable clinical outcome (4)(5). Because of such findings, the clinical demand for mutation testing has exploded recently in cancer diagnostics.

The specimens used for molecular testing range from large surgical resections to tiny fine-needle aspiration biopsies to cytology smears. Samples are submitted as either frozen or formalin-fixed, paraffin-embedded tissues, and the percentage of tumor cells varies substantially among different specimens. One of the major challenges that molecular diagnostics laboratories face is to detect mutations in samples with a low percentage of mutation-carrying tumor cells in a background of wild-type nonmalignant cells. The fact that the mutation-detection limit is approximately 20% for the gold standard of Sanger sequencing and approximately 5%–10% for pyrosequencing (6) necessitates implementation of tumor-enrichment strategies for samples with a small tumor component.

When tissue sections or smears on …
Dynamic eye convergence for head-mounted displays improves user performance in virtual environments (2012)

In Virtual Environments (VE), users are often facing tasks that involve direct manipulation of virtual objects at close distances, such as touching, grabbing, placement. In immersive systems that employ head-mounted displays these tasks could be quite challenging, due to lack of convergence of virtual cameras.
Desmethylselegiline, a Metabolite of Selegiline, Is an Irreversible Inhibitor of Monoamine Oxidase Type B in Humans (1997)

Selegiline, an irreversible and selective inhibitor of monoamine oxidase type B (MAO-B), is metabolized into desmethylselegiline, levomethamphetamine, and levoamphetamine. In animal experiments, desmethylselegiline also has been shown to be an irreversible inhibitor of MAO-B. This study investigated the inhibitory potential of MAO-B and the pharmacokinetics of desmethylselegiline in humans. A double-blind, crossover trial was performed to compare the effects of a single dose (10 mg) of selegiline or desmethylselegiline on MAO-B platelet activity. The urinary excretion of phenylethylamine, which is considered to be a parameter of MAO-B inhibition, also was measured. The concentrations of selegiline, desmethylselegiline, and their metabolites were measured in plasma after administration of the two compounds. Ten healthy volunteers participated in the study. There was a clear inhibition of platelet MAO-B by both compounds. Desmethylselegiline caused a 63.7 +/- 12.7% inhibition of platelet MAO-B compared with 96.4 +/- 3.9% caused by selegiline. The maximal inhibition by desmethylselegiline was reached significantly later after desmethylselegiline (time to reach maximal inhibition [tmax], 27 +/- 20 hours) than after selegiline administration (tmax, 1.4 +/- 1.4 hours). The platelet MAO-B activity returned to baseline levels within 2 weeks, thus reflecting the irreversible nature of the inhibition by both compounds. The cumulative 48-hour excretion of phenylethylamine was 33% lower after desmethylselegiline than after selegiline administration. All three major metabolites of selegiline could be detected in plasma after selegiline administration. Levoamphetamine was the only metabolite of desmethylselegiline. The area under the concentration-time curve from time 0 to 24 hours (AUC0-24) of desmethylselegiline was 33 times higher than that of selegiline, suggesting a better bioavailability of desmethylselegiline. Desmethylselegiline is an orally active, irreversible inhibitor of MAO-B and could possibly be used to treat Parkinson's disease in the same way as selegiline.
A Survey of Interactive Remote Rendering Systems (2015)

Remote rendering means rendering 3D graphics on a computing device and displaying the results on another computing device connected through a network. The concept was originally developed for sharing computing resources remotely. It has been receiving increasing attention from researchers in both academia and industry in recent years due to the proliferation of cloud computing and mobile devices. In this article, we survey the interactive remote rendering systems proposed in the literature, analyze how to improve the state of the art, and summarize the related technologies. The readers of this article will understand the history of remote rendering systems and obtain some inspirations of the future research directions in this area.
Distributed feedback InGaAsP/InP lasers with window region emitting at 1.5 µm range (1983)

Distributed feedback (DFB) InGaAsP/InP lasers with a window region formed at an end of the corrugated DFB region were made in order to overcome the problems inherent in the previous structures of DFB lasers with cleaved, sawed, etched, or AR-coated facets, or with an unexcited corrugation region. The window structure DFB lasers showed linear current versus output ( <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">I-L</tex> ) curves, in contrast to those with a hysteresis or a kink appearing in a DFB laser with an unexcited region. Suppression of Fabry-Perot (F-P) resonances due to the two facets were sufficient enough to keep a single longitudinal mode property by DFB up to high excitation level. CW operation up to 65°C was achieved at the 1.5 μm wavelength range. Axial modes concerning the corrugated resonator were measured at about the threshold current. A stop band of a DFB laser was clearly observed with two dominant modes and much smaller submodes, which almost agreed with the axial modes predicted from a basic DFB theory.
A Survey on Opportunistic Routing in Wireless Communication Networks (2015)

The great advances made in the wireless technology have enabled the deployment of wireless communication networks in some of the harshest environments such as volcanoes, hurricane-affected regions, and underground mines. In such challenging environments suffering from the lack of infrastructure, traditional routing is not efficient and sometimes not even feasible. Moreover, the exponential growth of the number of wireless connected devices has created the need for a new routing paradigm that could benefit from the potentials offered by these heterogeneous wireless devices. Hence, in order to overcome the traditional routing limitations, and to increase the capacity of current dynamic heterogeneous wireless networks, the opportunistic routing paradigm has been proposed and developed in recent research works. Motivated by the great interest that has been attributed to this new paradigm within the last decade, we provide a comprehensive survey of the existing literature related to opportunistic routing. We first study the main design building blocks of opportunistic routing. Then, we provide a taxonomy for opportunistic routing proposals, based on their routing objectives as well as the optimization tools and approaches used in the routing design. Hence, five opportunistic routing classes are defined and studied in this paper, namely, geographic opportunistic routing, link-state-aware opportunistic routing, probabilistic opportunistic routing, optimization-based opportunistic routing, and cross-layer opportunistic routing. We also review the main protocols proposed in the literature for each class. Finally, we identify and discuss the main future research directions related to the opportunistic routing design, optimization, and deployment.
Cu-free click cycloaddition reactions in chemical biology (2010)

Bioorthogonal chemical reactions are paving the way for new innovations in biology. These reactions possess extreme selectivity and biocompatibility, such that their participating reagents can form covalent bonds within richly functionalized biological systems--in some cases, living organisms. This tutorial review will summarize the history of this emerging field, as well as recent progress in the development and application of bioorthogonal copper-free click cycloaddition reactions.
Analysis of IL-17+cells in facet joints of patients with spondyloarthritis suggests that the innate immune pathway might be of greater relevance than the Th17-mediated adaptive immune response (2011)

Our data suggest an important role for IL-17 in the inflammatory processes in AS. However, the innate immune pathway might be of greater relevance than the Th17-mediated adaptive immune response.
Structures and Properties of Commercial Maltodextrins from Corn, Potato, and Rice Starches (2000)

Commercial maltodextrins derived from corn, potato, and rice starches were characterized for their chemical structures and physicochemical properties. Rice maltodextrin consisted of more low molecular-weight (MW) saccharides and potato maltodextrin consisted of more high MW saccharides. Debranched rice maltodextrin had a significantly higher content of saccharides with degree of polymerization (DP) less than 10. On the other hand, debranched potato maltodextrin had a significantly higher content of saccharides with DP greater than 20. Rice maltodextrin had higher protein and lipid contents and exhibited very high viscosity at 40% concentration, which might be caused by the retrograded amylose contained in rice maltodextrin. It is believed that the longer average chain lengths of potato maltodextrin resulted in greater retrogradation, and the shorter chains in rice maltodextrin resulted in lower maximum freeze-concentrated glass transition temperature. The differences in structure of maltodextrins from different botanical sources determine their physicochemical properties.
Biomechanical Walking Pattern Changes in the Fit and Healthy Elderly (1990)

A descriptive study of the biomechanical variables of the walking patterns of the fit and healthy elderly compared with those of young adults revealed several significant differences. The walking patterns of 15 elderly subjects, selected for their active life style and screened for any gait- or balance-related pathological conditions, were analyzed. Kinematic and kinetic data for a minimum of 10 repeat walking trials were collected using a video digitizing system and a force platform. Basic kinematic analyses and an inverse dynamics model yielded data based on the following variables: temporal and cadence measures, heal and toe trajectories, joint kinematics, joint moments of force, and joint mechanical power generation and absorption. Significant differences between these elderly subjects and a database of young adults revealed the following: the same cadence but a shorter step length, an increased double-support stance period, decreased push-off power, a more flat-footed landing, and a reduction in their "index of dynamic balance." All of these differences, except reduction in index of dynamic balance, indicate adaptation by the elderly toward a safer, more stable gait pattern. The reduction in index of dynamic balance suggests deterioration in the efficiency of the balance control system during gait. Because of these significant differences attributable to age alone, it is apparent that a separate gait database is needed in order to pinpoint falling disorders of the elderly.
Simplified Synthetic TMC‐95A/B Analogues Retain the Potency of Proteasome Inhibitory Activity (2003)

The proteasome regulates diverse intracellular processes, including cell-cycle progression, antigen presentation, and inflammatory response. Selective inhibitors of the proteasome have great therapeutic potential for the treatment of cancer and inflammatory disorders. Natural cyclic peptides TMC-95A and B represent a new class of noncovalent, selective proteasome inhibitors. To explore the structure-activity relationship of this class of proteasome inhibitors, a series of TMC-95A/B analogues were prepared and analyzed. We found that the unique enamide functionality at the C8 position of TMC-95s can be replaced with a simple allylamide. The asymmetric center at C36 that distinguishes TMC-95A from TMC-95B but which necessitates a complicated separation of the two compounds can be eliminated. Therefore, these findings could lead to the development of more accessible simple analogues as potential therapeutic agents.
Composition of sugar cane, energy cane, and sweet sorghum suitable for ethanol production at Louisiana sugar mills (2010)

A challenge facing the biofuel industry is to develop an economically viable and sustainable biorefinery. The existing potential biorefineries in Louisiana, raw sugar mills, operate only 3 months of the year. For year-round operation, they must adopt other feedstocks, besides sugar cane, as supplemental feedstocks. Energy cane and sweet sorghum have different harvest times, but can be processed for bio-ethanol using the same equipment. Juice of energy cane contains 9.8% fermentable sugars and that of sweet sorghum, 11.8%. Chemical composition of sugar cane bagasse was determined to be 42% cellulose, 25% hemicellulose, and 20% lignin, and that of energy cane was 43% cellulose, 24% hemicellulose, and 22% lignin. Sweet sorghum was 45% cellulose, 27% hemicellulose, and 21% lignin. Theoretical ethanol yields would be 3,609 kg per ha from sugar cane, 12,938 kg per ha from energy cane, and 5,804 kg per ha from sweet sorghum.
Hyperglycemia inhibits endothelial nitric oxide synthase activity by posttranslational modification at the Akt site (2001)

Endothelial nitric oxide synthase (eNOS) is activated by phosphorylation of serine 1177 by the protein kinase Akt/PKB. Since hyperglycemia-induced mitochondrial superoxide overproduction increases O-linked N-acetylglucosamine modification and decreases O-linked phosphorylation of the transcription factor Sp1, the effect of hyperglycemia and the hexosamine pathway on eNOS was evaluated. In bovine aortic endothelial cells, hyperglycemia inhibited eNOS activity 67%, and treatment with glucosamine had a similar effect. Hyperglycemia-associated inhibition of eNOS was accompanied by a twofold increase in O-linked N-acetylglucosamine modification of eNOS and a reciprocal decrease in O-linked serine phosphorylation at residue 1177. Both the inhibition of eNOS and the changes in its post-translational modifications were reversed by antisense inhibition of glutamine:fructose-6-phosphate amidotransferase, the rate-limiting enzyme of the hexosamine pathway, or by blocking mitochondrial superoxide overproduction with uncoupling protein-1 (UCP-1) or manganese superoxide dismutase (MnSOD). Immunoblot analysis of cells expressing myc-tagged wild-type human eNOS confirmed the reciprocal increase in O-linked N-acetylglucosamine and decrease in O-linked serine 1177 phosphorylation in response to hyperglycemia. In contrast, when myc-tagged human eNOS carried a mutation at the Akt phosphorylation site (Ser1177), O-linked N-acetylglucosamine modification was unchanged by hyperglycemia and phospho-eNOS was undetectable. Similar changes in eNOS activity and covalent modification were found in aortae from diabetic animals. Chronic impairment of eNOS activity by this mechanism may partly explain the accelerated atherosclerosis of diabetes.
Extracting Figures and Captions from Scientific Publications (2018)

Figures and captions convey essential information in scientific publications. As such, there is a growing interest in mining published figures and in utilizing their respective captions as a source of knowledge. There is also much interest in image captioning systems that can automatically generate captions for images, whose training requires large datasets of image-caption pairs. Notably, the first fundamental step of obtaining figures and captions from publications is neither well-studied nor yet well-addressed. In this paper, we introduce a new and effective system for figure and caption extraction, PDFigCapX. Unlike current methods that extract figures by handling raw encoded contents of PDF documents, we separate text from graphical contents and utilize layout information to detect and disambiguate figures and captions. Files containing the figures and their associated captions are then produced as output to the end-user. We test PDFigCapX on both a previously used generic dataset and on two new sets of publications within the biomedical domain. Our experiments and results show a significant improvement in performance compared to the state-of-the-art, and demonstrate the effectiveness of our approach. Our system will be available for use at: https://www.eecis.udel.edu/~compbio/PDFigCapX.
Elimination of the Acetaminophen Interference in an Implantable Glucose Sensor (1994)

Acetaminophen has been one of the most serious electrochemical interferences to oxidase-based amperometric biosensors that measure H2O2. A study was carried out to investigate various polymer materials for their selectivity as the sensor inner membrane. A composite membrane of cellulose acetate and Nafion was found to eliminate acetaminophen and other electrochemical interferences effectively while at the same time maintaining reasonable diffusivity for hydrogen peroxide. The excellent in vivo performance of the sensor was attributed not only to significantly reduced steady-state sensitivity to acetaminophen but also to very slow acetaminophen response. These features, combined with rapid acetaminophen clearance pharmacokinetics, led to the decreased response as demonstrated in the rat.
Structure and stabilization of the Hendra virus F glycoprotein in its prefusion form (2015)

Hendra virus (HeV) is one of the two prototypical members of the Henipavirus genus of paramyxoviruses, which are designated biosafety level 4 (BSL-4) organisms due to the high mortality rate of Nipah virus (NiV) and HeV in humans. Paramyxovirus cell entry is mediated by the fusion protein, F, in response to binding of a host receptor by the attachment protein. During posttranslational processing, the fusion peptide of F is released and, upon receptor-induced triggering, inserts into the host cell membrane. As F undergoes a dramatic refolding from its prefusion to postfusion conformation, the fusion peptide brings the host and viral membranes together, allowing entry of the viral RNA. Here, we present the crystal structure of the prefusion form of the HeV F ectodomain. The structure shows very high similarity to the structure of prefusion parainfluenza virus 5 (PIV5) F, with the main structural differences in the membrane distal apical loops and the fusion peptide cleavage loop. Functional assays of mutants show that the apical loop can tolerate perturbation in length and surface residues without loss of function, except for residues involved in the stability and conservation of the F protein fold. Structure-based disulfide mutants were designed to anchor the fusion peptide to conformationally invariant residues of the F head. Two mutants were identified that inhibit F-mediated fusion by stabilizing F in its prefusion conformation.