gebhart/patrepeval huggingface dataset:
Antiviral Activity of Uridine Derivatives of 2-Deoxy Sugars against Tick-Borne Encephalitis Virus (2019)

Tick-borne encephalitis virus (TBEV) is a causative agent of tick-borne encephalitis (TBE), one of the most important human infections involving the central nervous system. Although effective vaccines are available on the market, they are recommended only in endemic areas. Despite many attempts, there are still no specific antiviral therapies for TBEV treatment. Previously, we synthesized a series of uridine derivatives of 2-deoxy sugars and proved that some compounds show antiviral activity against viruses from the Flaviviridae and Orthomyxoviridae families targeting the late steps of the N-glycosylation process, affecting the maturation of viral proteins. In this study, we evaluated a series of uridine derivatives of 2-deoxy sugars for their antiviral properties against two strains of the tick-borne encephalitis virus; the highly virulent TBEV strain Hypr and the less virulent strain Neudoerfl. Four compounds (2, 4, 10, and 11) showed significant anti-TBEV activity with IC50 values ranging from 1.4 to 10.2 µM and low cytotoxicity. The obtained results indicate that glycosylation inhibitors, which may interact with glycosylated membrane TBEV E and prM proteins, might be promising candidates for future antiviral therapies against TBEV.
The SMART project - speed measurement validation in real traffic condition (2005)

In this paper an automatic validation system for speed measurement devices is described. The system was specifically designed to test speed within the SMART Project, an experimental survey on traffic monitoring devices led by ANAS, the Italian Road Agency. A matrix of infrared sensors was used to implement the system and allow accurate speed measurements under real traffic condition, without road restraints. Special reflecting devices were developed in order to separate single lane measurements and reveal vehicles crossing among them. A GPS in-vehicle speed measurement device with high accuracy was used to test and validate the system.
Reconstruction-plane-dependent weighted FDK algorithm for cone beam volumetric CT (2005)

The original FDK algorithm has been extensively employed in medical and industrial imaging applications. With an increased cone angle, cone beam (CB) artifacts in images reconstructed by the original FDK algorithm deteriorate, since the circular trajectory does not satisfy the so-called data sufficiency condition (DSC). A few “circular plus” trajectories have been proposed in the past to reduce CB artifacts by meeting the DSC. However, the circular trajectory has distinct advantages over other scanning trajectories in practical CT imaging, such as cardiac, vascular and perfusion applications. In addition to looking into the DSC, another insight into the CB artifacts of the original FDK algorithm is the inconsistency between conjugate rays that are 180° apart in view angle. The inconsistence between conjugate rays is pixel dependent, i.e., it varies dramatically over pixels within the image plane to be reconstructed. However, the original FDK algorithm treats all conjugate rays equally, resulting in CB artifacts that can be avoided if appropriate view weighting strategy is exercised. In this paper, a modified FDK algorithm is proposed, along with an experimental evaluation and verification, in which the helical body phantom and a humanoid head phantom scanned by a volumetric CT (64 x 0.625 mm) are utilized. Without extra trajectories supplemental to the circular trajectory, the modified FDK algorithm applies reconstruction-plane-dependent view weighting on projection data before 3D backprojection, which reduces the inconsistency between conjugate rays by suppressing the contribution of one of the conjugate rays with a larger cone angle. Both computer-simulated and real phantom studies show that, up to a moderate cone angle, the CB artifacts can be substantially suppressed by the modified FDK algorithm, while advantages of the original FDK algorithm, such as the filtered backprojection algorithm structure, 1D ramp filtering, and data manipulation efficiency, can be maintained.
Palladium(<scp>ii</scp>)-catalysed regioselective synthesis of 3,4-disubstituted quinolines and 2,3,5-trisubstituted pyrroles from alkenes via anti-Markovnikov selectivity (2015)

A novel strategy has been identified for the regioselective synthesis of 3,4-disubstituted quinolines and 2,3,5-trisubstituted pyrroles from simple alkenes via anti-Markovnikov selectivity under palladium catalysis. The salient features are synthesis of two different heterocycles, readily available starting materials, broad substrate scope, moderate to good yields and use of molecular oxygen as a terminal oxidant.
Data analysis methods for evaluating lithographic performance (1997)

Lithographic improvements obtained from process modifications or application of optical enhancement techniques can often be obscured within experimental noise and inconsistent data analysis techniques. At IBM, the need for a common platform for the accurate analysis of lithographic data led to the development of a new software analysis package entitled LEOPOLD. In this article, the exposure-defocus methodology taken by LEOPOLD for accurate calculation of the total lithographic process window in the presence of experimental noise is outlined; the extension of this method to the evaluation of the common process window through applications in the areas of optical proximity effects, analysis of optical enhancement techniques, and across-field exposure tool characterization is also demonstrated.
Biosynthesis of the polysialic acid capsule in <i>Escherichia coli</i> K1. Cold inactivation of sialic acid synthase regulates capsule expression below 20°C<sup>*</sup> (1990)

When neuroinvasive Escherichia coli K1 cells are grown at temperatures below 20 degrees C, they fail to synthesize the alpha-2,8-linked polysialic acid (polySia) capsule. The objective of this study was to use a genetic and biochemical approach to analyse why capsule expression was defective at cold temperatures. The strategy was to construct E.coli K1-derived mutants with defects in activation and degradation of Sia. The inability to degrade Sia because of a defect in the Sia-specific aldolase permitted accurate quantitation of Sia and CMP-Sia. Strains EV5 and EV90 possessed a defective CMP-Sia synthetase and were unable to activate Sia. These mutants were then used to study how synthesis of Sia, CMP-Sia, and the polySia capsule was affected by growth at 15 degrees C. In contrast to wild type strains, the mutants accumulated Sia in considerable quantities (up to 100 nmol mg protein-1) at 37 degrees C. However, no Sia was detected after growth at 15 degrees C. A temperature upshift experiment showed that the intracellular concentration of Sia increased ca. 3-fold within 5-10 min after shift from 15 to 37 degrees C, even in the presence of inhibitors of protein synthesis or transcription initiation. An in vitro assay for Sia synthase showed that Sia was synthesized at 37 degrees C in cell-free extracts from both 37 and 15 degrees C grown cells, but that no synthesis occurred when the same extracts were assayed at 15 degrees C.(ABSTRACT TRUNCATED AT 250 WORDS)
Influence of process pressure on the growth of hydrocarbon films under direct dc bias in an electron cyclotron resonance plasma (1998)

The effects of pressure on the deposition of hydrogenated amorphous carbon (a-C:H) thin films using the electron cyclotron resonance chemical vapor deposition (ECR-CVD) technique are reported. In this study, the ions were accelerated under a constant direct dc bias achieved through a screen grid positioned above the substrate. The deposition pressure was varied to study its effects on the plasma environment under the ECR conditions and also on the properties of the films deposited. It was found that changing the process pressure has a very significant effect on the properties of the films deposited. The hardness and the optical gap of the films were noted to increase with pressure. The sp3 content in the films, as deduced from their Raman spectra, was also observed to increase. The results obtained in this study show that the plasma chemistry, in addition to the ion energy, plays a very significant role in determining the properties of the films deposited. The denser plasma created under the ECR condition at higher pressure, accompanied by the presence of a relatively large amount of atomic hydrogen resulting in enhanced plasma etching of the films, is believed to lead to the results observed. Comparisons have also been made between films deposited under rf induced bias and direct dc bias in the ECR-CVD system. The difference in the characteristics observed can be attributed to the narrower ion energy distribution in the case of direct dc bias.
S100A1 gene transfer: a strategy to strengthen engineered cardiac grafts (2004)

S100A1 gene transfer in EHT is feasible and augments contractile performance, while characteristic physiological features of EHT remain unchanged. Thus, specific genetic manipulation of tissue constructs prior to implantation should be part of an improved tissue replacement strategy in heart failure.
Epilepsy-Related Ligand/Receptor Complex LGI1 and ADAM22 Regulate Synaptic Transmission (2006)

Abnormally synchronized synaptic transmission in the brain causes epilepsy. Most inherited forms of epilepsy result from mutations in ion channels. However, one form of epilepsy, autosomal dominant partial epilepsy with auditory features (ADPEAF), is characterized by mutations in a secreted neuronal protein, LGI1. We show that ADAM22, a transmembrane protein that when mutated itself causes seizure, serves as a receptor for LGI1. LGI1 enhances AMPA receptor-mediated synaptic transmission in hippocampal slices. The mutated form of LGI1 fails to bind to ADAM22. ADAM22 is anchored to the postsynaptic density by cytoskeletal scaffolds containing stargazin. These studies in rat brain indicate possible avenues for understanding human epilepsy.
A Very Compact 1.0-μm CMOS SC Multirate 2-D Image Filter (1996)

This paper describes the design and integrated circuit implementation of a very compact switched-capacitor two-dimensional filter for image processing applications. A prototype chip realized in a 1.0-μm double-poly CMOS process consumes only half of the silicon area and power consumption that would have been required using previously reported solutions. Experimental results are shown to be in good agreement with theoretical results.
Boron Fluoride Catalyzed Addition of Aliphatic Anhydrides to Aldehydes<sup>1</sup> (1950)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBoron Fluoride Catalyzed Addition of Aliphatic Anhydrides to Aldehydes1Eugene H. Man, James J. Sanderson, and Charles R. HauserCite this: J. Am. Chem. Soc. 1950, 72, 2, 847–848Publication Date (Print):February 1, 1950Publication History Published online1 May 2002Published inissue 1 February 1950https://pubs.acs.org/doi/10.1021/ja01158a053https://doi.org/10.1021/ja01158a053research-articleACS PublicationsRequest reuse permissionsArticle Views135Altmetric-Citations20LEARN 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
Translational Repressor Activity Is Equivalent and Is Quantitatively Predicted by in Vitro RNA Binding for Two Iron-responsive Element-binding Proteins, IRP1 and IRP2 (1995)

Iron regulatory proteins (IRPs) bind to specific RNA stem-loop structures known as iron-responsive elements (IREs) which mediate the post-transcriptional regulation of many genes of iron metabolism. Most studies have focused on the role of IRP1, which has previously been shown to bind with high affinity to IREs and mediate repression of in vitro translation of ferritin mRNAs. More recently, a second IRP has been identified that is expressed in all tissues and that binds IREs (Rouault, T. A., Haile, D. H., Downey, W. E., Philpott, C. C., Tang, C., Samaniego, F., Chin, J., Paul, I., Orloff, D., Harford, J. B., and Klausner, R. D. (1992) BioMetals 5, 131-140; Henderson, B. R., Seiser, C., and Kuhn, L. C. (1993) J. Biol. Chem. 268, 27327-27334; Guo, B., Yu, Y., and Leibold, E. A. (1994) J. Biol. Chem. 269, 24252-24260; Samaniego, F., Chin, J., Iwai, K., Rouault, T. A., and Klausner, R. D. (1994) J. Biol. Chem. 269, 30904-30910). Here we report that purified recombinant IRP2 inhibits translation of ferritin mRNAs with a molar efficacy equal to that of recombinant IRP1. There is a quantitative correlation between binding to isolated RNA target motifs, as judged by gel retardation assays, and translational repressor function as assayed in an in vitro translation system. In contrast to IRP1, IRP2 is not inactivated for RNA binding by alkylation with N-ethylmaleimide or phenylmaleimide, and as we would therefore predict, IRP2 treated with N-ethylmaleimide remains an effective repressor of ferritin translation. As IRP1 and IRP2 clearly have equal capability of mediating translational repression in vitro, the contributions of both IRPs to overall regulation must be considered in describing the pathways of iron regulated gene expression in individual cells.
On the constrained synthesis of array patterns with applications to circular and arc arrays (1984)

Synthesis of array patterns involving optimization with linear and nonlinear constraints is considered. The general solution for the composite weight vector can be decomposed into a part which satisfies the linear constraints and another lying orthogonal to it. This decomposition is shown to yield simple solutions to several beam optimization problems including some with nonlinear constraints. A geometrical derivation of this result is presented which also provides new insights into the mechanism of null-steering via linear constraints. Application of this approach in conjunction with some search algorithms to the synthesis of optimum array patterns with prescribed narrow or broad nulls is shown to yield interesting and useful solutions. The results are illustrated by considering the design of "circular" and "arc" arrays.
Accuracy of Intraoperative Gross Examination of Surgical Margin Status in Women Undergoing Partial Mastectomy for Breast Malignancy (2005)

Margin status is an important prognostic factor for local recurrence after partial mastectomy for breast malignancy. Options for intraoperative evaluation of margin status include gross examination of the specimen, frozen section, and "touch preparation" cytology. This study evaluates the accuracy of gross examination without other intraoperative pathological analysis as a method of determining margin status. Records of 254 consecutive patients undergoing partial mastectomy for 255 breast malignancies (199 invasive, 56 DCIS) over 6 years were analyzed retrospectively. All women underwent en bloc excision of the primary lesion with gross examination of margin status by the surgeon and pathologist. All suspicious areas were reexcised, and the specimen was inked, serially sectioned at 2-3 mm intervals and examined with hematoxylin and eosin (H&E) stains. Specimens with tumor <2 mm from a margin were considered margin-positive and those with all tumor > or =2 mm from the margin were designated margin-negative. One hundred fourteen (45%) of the 255 segmental resections were considered to have grossly tumor-free margins, and intraoperative reexcision was not performed. Ninety-six (84%) of these specimens had histologically negative margins. Gross examination prompted intraoperative reexcision in 141 (55%) cases. Ninety-five (67%) of these 141 resections had tumor-free margins on histopathology. Overall, the final margin was involved in 64 of the 255 partial mastectomies. Seventeen (27%) women with initially margin-positive resections underwent mastectomy, while 46 (72%) underwent reexcision, which was margin-negative in 41 (89%). After a median follow-up of 42 months, there have been eight (3.5%) local recurrences. The initial margin-positive rate was similar in ductal carcinoma in situ (DCIS) (30%) and invasive carcinoma (24%). Margin status was correlated with nodal status; there was no correlation with age, tumor size, grade hormone receptor status, or type of diagnostic biopsy. Gross examination of the resection specimen does not reflect margin status in at least 25 per cent of women undergoing partial mastectomy for breast malignancy. Other techniques for evaluation of margin status should be considered to reduce the need for reexcision of involved margins. We are currently designing a prospective clinical trial to examine the efficacy of new techniques for intraoperative evaluation of margin status.
Directed Evolution of Rubisco in <i>Escherichia coli</i> Reveals a Specificity-Determining Hydrogen Bond in the Form II Enzyme (2007)

Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) occupies a critical position in photosynthetic CO2-fixation and consequently has been the focus of intense study. Crystal-structure-guided site-directed mutagenesis studies have met with limited success in engineering kinetic improvements to Rubisco, highlighting our inadequate understanding of structural constraints at the atomic level that dictate the enzyme's catalytic chemistry. Bioselection provides an alternative random mutagenic approach that is useful for identifying and elucidating imperceptible structure-function relationships. Using the dimeric Form II Rubisco from Rhodospirillum rubrum, its gene (rbcM) was randomly mutated and introduced under positive selection into Escherichia coli cells metabolically engineered to be dependent on Rubisco to detoxify its substrate ribulose 1,5-bisphosphate. Thirteen colonies displaying improved fitness were isolated, and all were found to harbor mutations in rbcM at one of two codons, histidine-44 or aspartate-117, that are structurally adjacent amino acids located about 10 A from the active site. Biochemical characterization of the mutant enzymes showed the mutations reduced their CO2/O2 specificity by 40% and decreased their carboxylation turnover rate by 20-40%. Structural analyses showed histidine-44 and aspartate-117 form a hydrogen bond in R. rubrum Rubisco and that the residues are conserved among other Form II Rubiscos. This study demonstrated the utility of directed evolution in E. coli for identifying catalytically relevant residues (in particular nonobvious residues disconnected from active site residues) and their potential molecular interactions that influence Rubisco's catalytic chemistry.
Surface periodic structures induced by pulsed laser irradiation of fullerite (1996)

Fullerite surface modifications induced by 1064 and 266 nm pulsed laser irradiation have been studied by scanning electron microscopy. The formation of micropatterns with a well-defined periodicity is reported. The morphology of the periodic nanostructures can be controlled by varying the laser fluence, the angle of incidence, and the wavelength. The different patterns observed for infrared and ultraviolet irradiation suggest that electronic and thermal effects are responsible of the formation of the periodic structures.
Developmental regulation of c-myb in normal myeloid progenitor cells. (1985)

Hematopoietic tissues and some leukemic cell lines express elevated levels of c-myb transcripts. We have separated a subpopulation of chicken embryo yolk sac cells that represents about 5% of the yolk sac hematopoietic cells and appears to contain all of the detectable c-myb transcripts. The level of myb expression in this cell population is higher than previously reported for any normal cell population and is in the range of that found in cells transformed by avian myeloblastosis virus and E26 virus. Since the myb gene probe used also detects full-length viral transcripts as well as the v-myb mRNA, it appears that the level of expression of c-myb in this normal population may exceed that found in some transformed cell populations that depend on v-myb to maintain the transformed phenotype. This c-myb-expressing cell population has been identified as primarily M-CFC, the committed progenitor for the macrophage lineage. As cells differentiate to the promonocyte stage there is an abrupt decrease in c-myb expression of greater than 100 fold. These studies thus describe a normal cell population that expresses c-myb at levels similar to the level of v-myb in cells that depend on v-myb for the maintenance of their transformed phenotype. Furthermore, these studies provide direct evidence for the developmental regulation of c-myb during the process of normal macrophage differentiation.
Semantic Mapping Using Automatic Word Alignment and Semantic Role Labeling (2011)

To facilitate the application of semantics in statistical machine translation, we propose a broad-coverage predicate-argument structure mapping technique using automated resources. Our approach utilizes automatic syntactic and semantic parsers to generate Chinese-English predicate-argument structures. The system produced a many-to-many argument mapping for all PropBank argument types by computing argument similarity based on automatic word alignment, achieving 80.5 % F-score on numbered argument mapping and 64.6 % F-score on all arguments. By measuring predicate-argument structure similarity based on the argument mapping, and formulating the predicate-argument structure mapping problem as a linear-assignment problem, the system achieved 84.9 % F-score using automatic SRL, only 3.7 % F-score lower than using gold standard SRL. The mapping output covered 49.6 % of the annotated Chinese predicates (which contains predicateadjectives that often have no parallel annotations in English) and 80.7 % of annotated English predicates, suggesting its potential as a valuable resource for improving word alignment and reranking MT output. 1
U.S. Drug Policy: Shaping Relations With Latin America (2014)

Recent state-level changes in drug policy have raised the prospect that similar changes in federal policy may one day follow. Any such changes will have profound effects on U.S. relations with its neighbors to the south. This thesis attempts to analyze the effects of U.S. drug policy on the overall character of U.S. relations with Latin America. U.S. policy and actions have created a pattern of relationships and side effects in Latin America that can help predict how a continuation, or a change, of current U.S. drug policy may alter U.S. relations with Latin America and influence social and political conditions within the major drug-producing countries of the region. This thesis also seeks to explore policy alternatives to curtail drug related crimes and health issues, which current prohibitive policies exacerbate, and outlines steps to help new policies reach actual implementation.