gebhart/patrepeval huggingface dataset:
Early endonuclease-mediated evasion of RNA sensing ensures efficient coronavirus replication (2017)

Coronaviruses are of veterinary and medical importance and include highly pathogenic zoonotic viruses, such as SARS-CoV and MERS-CoV. They are known to efficiently evade early innate immune responses, manifesting in almost negligible expression of type-I interferons (IFN-I). This evasion strategy suggests an evolutionary conserved viral function that has evolved to prevent RNA-based sensing of infection in vertebrate hosts. Here we show that the coronavirus endonuclease (EndoU) activity is key to prevent early induction of double-stranded RNA (dsRNA) host cell responses. Replication of EndoU-deficient coronaviruses is greatly attenuated in vivo and severely restricted in primary cells even during the early phase of the infection. In macrophages we found immediate induction of IFN-I expression and RNase L-mediated breakdown of ribosomal RNA. Accordingly, EndoU-deficient viruses can retain replication only in cells that are deficient in IFN-I expression or sensing, and in cells lacking both RNase L and PKR. Collectively our results demonstrate that the coronavirus EndoU efficiently prevents simultaneous activation of host cell dsRNA sensors, such as Mda5, OAS and PKR. The localization of the EndoU activity at the site of viral RNA synthesis-within the replicase complex-suggests that coronaviruses have evolved a viral RNA decay pathway to evade early innate and intrinsic antiviral host cell responses.
FlowRank (2010)

This paper describes a new approach to identify relevant flow records in large scale flow dataset. We propose a method that leverages the well known page rank algorithm in order to extract the most relevant flows. We introduce a dependency relation that uses a simple and efficient causal relationship. The strength of this dependency is determined by time related information. We have tested our method on datasets coming from our campus network.
Structural studies on the diglyceride-mediated activation of protein kinase C. (1988)

Diglyceride analogs were studied with respect to their abilities to activate protein kinase C (Ca2+- and phospholipid-dependent protein kinase) in the presence of low calcium and phospholipid. Analogs which lacked either a free hydroxyl group at the 3 position or an ester moiety at the 1 position were without activity. It was concluded that the hydrophilic moieties of the active diglycerides are crucial for activity. However, diglyceride analogs containing additional hydrophilic moieties in one of the acyl side chains did not exhibit enhanced activity when compared to diglycerides containing two fatty acyl groups. Diglyceride analogs with a modified glycerol backbone were also studied. Homologous diglycerides with either one or two methylene groups between the 3-methylene group of the diglyceride and the hydroxyl group possessed markedly reduced activities when compared to the appropriate unmodified diglyceride. Isomers of these homologues which contained either a methyl group at the 1 position, or dimethyl groups incorporated at the 1 and 3 positions, were virtually without activity. Where studied, none of the diglyceride analogs prepared possessed antagonist activity. The results of these experiments are discussed with respect to the extreme specificity observed.
EHRLICH ASCITES TUMOR (EAT) CHALONE EFFECTS ON NASCENT DNA SYNTHESIS AND DNA POLYMERASE ALPHA AND BETA (1976)

EAT chalone effects on nascent DNA synthesis and DNA polymerase were examined. Concentration related inhibition of 3H-thymidine (3H-TdR) incorporation into EAT cell DNA was noted over a chalone range of 50-200 mug/ml. RNA synthesis was not affected, but protein synthesis decreased an average of 82% during 3 hr. Nascent DNA pulse-labeled for 2 min was normally incorporated into bulk DNA in the presence of chalone, but crude alpha- and beta-polymerase activities were inhibited. Crude DNA polymerase for C3H mouse kidney and spleen was also partially inhibited by EAT chalone, suggesting non-specific inhibition of DNA polymerase. Preincubation studies of chalone with crude EAT DNA polymerase or 'gapped' DNA primer had no effect on chalone activity. Chalone may control mitotic activity by inhibiting alpha- and beta-polymerase activity, thereby decreasing nascent DNA synthesis. Nascent DNA is incorporated normally into bulk DNA in the presence of chalone, indicating the DNA ligase is not inhibited.
Time domain simulation of electromagnetic cloaking structures with TLM method (2008)

The increasing interest in invisible cloaks has been prompted in part by the availability of powerful computational resources which permit numerical studies of such a phenomenon. These are usually carried out with commercial software. We report here a full time domain simulation of cloaking structures with the Transmission Line Modeling (TLM) method. We first develop a new condensed TLM node to model metamaterials in two dimensional situations; various results are then presented, with special emphasis on what is not easily achievable using commercial software.
Structural and photoluminescence properties of growth-induced InAs island columns in GaAs (1996)

InAs quantum dots layers produced by growth-induced islanding are vertically stacked with a variable thickness GaAs spacer layer. Using transmission electron microscopy, dense planar arrays of randomly ordered InAs islands are found to be vertically aligned in columns. We have compared single, 2, 5, and 10 layers of InAs islands and the vertical alignment is maintained. Atomic force microscopy shows the island size is unchanged throughout the layering process. 8 K photoluminescence shows a spectral peak shift and linewidth narrowing that we associate with electronic coupling within the columns. Variations in the GaAs spacer region produce spectral changes that are consistent with this coupling.
Synthesis of (2<i>S</i>,4<i>S</i>)-4-Hydroxyproline from D-Glucose (2012)

Abstract Diacetone-D-glucose 1 gives 3- O -methylxanthate 2 on reaction with NaH/Me I. Reductive deoxygenation of compound 2 by Bu3SnH gives the corresponding 3-deoxy glucose derivative 3 and on acid-catalyzed regioselective deprotection of C-5,6-acetonide gives the diol 4. The diol on oxidative cleavage with NaIO4 gives the aldehyde 5, which on further condensation with benzylamine followed by reduction with NaBH4 gives the amine 7. Z-Protection of the amine followed by methanolysis gives methyl furanoside 9. Reaction of 9 with methanesulfonyl chloride/Et3N gives the corresponding C-3-O-mesylate derivative 10. Catalytic hydrogenation of compound 10 (Pd/C/H2/MeOH 3 kg) gives bicyclic oxaazo compound 11, due to deprotection of the N-benzyl- and Z-protecting groups and intramolecular nucleophilic displacement of the C-2- O-mesylate by the C-5 amine in a one-pot reaction. Z-Protection of the amine 11 followed by acid-catalyzed hydrolysis gives acetal 13. Reduction of acetal by use of NaBH4 gives Z-prolinol 14. Selective oxidation of diol 14 by (2,2,6,6-tetramethylpiperidin-1-yl)-oxyl (TEMPO)/[(bis)(acetoxy)iodo]benzene (BAIB) and NaClO2/NaH2PO4, followed by Z-deprotection, gives the title compound I in 3.5% overall yield from D-glucose.
Adaptive Fuzzy Logic Control of a Single-Link Flexible Arm. (1997)

Fuzzy logic was employed in the vibration control of a single-link flexible arm. The control system has two feedback loops:one basic fuzzy control(BFC)loop to control the hub position and another loop to regulate the tip point vibration by either BFC or adaptive fuzzy control(AFC). The experimental results reveal that BFC is simpler and it requires less computing time, but the gains need to be found by a trial-and-error procedure. On the other hand, the AFC can generate and modify the control rules according to the performance of the system and it demands no tuning on the control gains for different operating ranges. Both the BFC and AFC are effective in suppressing the tip vibration and for adaptation to payload change.
5-substituted 2'-fluoro-arabinonucleosides as potential antiviral agents. (1987)

In order to study the electronic effects of 5-substituents of 2'-fluoro-ara-U on antiviral activity, eight nucleosides were synthesized and screened for their activity. Preliminary in vitro studies revealed that 5-thiocyano-, 5-hydroxy- and 5-formyl-ara-U are moderately active against HSV-1, HSV-2 and VZV, but they are also cytotoxic. None of these showed significant activity against CMV.
Binary pattern classification using optical phase conjugation (1986)

An elementary binary pattern classifier has n binary input variables and one binary output variable. The input variables may be identified with image pixels so that there are 2n possible input patterns. Classification or specification of the binary output is required for m of these patterns; the remaining patterns are do not cares. For m > 2n and large n (e.g., n ≥ 64), classifiers using all-electronic combinatorial logic techniques generally require numerous decision elements and complex interconnections. These requirements may lead to limited performance in areas such as processing speed and noise tolerance. Classifiers based on holographic associative memory techniques and the use of optical phase conjugation have potential for providing substantial performance improvements in these areas. In particular, analytical and computer simulation results indicate that phase conjugation with thresholded gain may significantly impove the ability of holographic associative memory processors to correctly classify numerous noisy or highly cross-correlated binary patterns. This indication may be attributed mainly to the fact that an additional well-interconnected decision surface can be inserted in a classifier by a thresholded phase conjugator.
The Nativeaccent™ pronunciation tutor: measuring success in the real world (2007)

This paper describes real user assessment of NativeAccent TM , a pronunciation tutor using automatic speech recognition that is a commercial product. It describes the product and discusses the issues involved in assessments of real users in real situations, such as assessments based on the customer's own criteria instead of more academic measures, and the variations in the customers' measures. Results in one study show that subjects who used NativeAccent TM did more than twice as well as the control group while both groups had human instruction. The implications of these results are discussed in light of other measures and real world considerations.
<b>Ventricular Tachycardia After Myocardial Infarction</b>: From Arrhythmia Surgery to Catheter Ablation (1995)

Ventricular tachycardia due to prior myocardial infarction is caused by reentry. Intraoperative mapping at the time of arrhythmia surgery has shown that the reentry circuits are diverse in size and location. Many circuits are large, extending over several square centimeters. Endocardial excision guided by activation sequence mapping, fractionated sinus rhythm electrograms, or visual identification of scarred subendocardium renders 69% to 95% of patients free from inducible ventricular tachycardia, but with an operative mortality that exceeds 8% at most centers. Catheter ablation is difficult due to limitations of catheter mapping, relatively small size of lesions produced with current techniques, and limited access to intramural and epicardial portions of the reentry circuits. Many problems need to be overcome for catheter ablation to achieve success comparable to that of surgery. At present, only hemodynamically tolerated ventricular tachycardias can be mapped. Progress is being made, and it is likely that catheter ablation will become a viable therapy for subgroups of patients with postmyocardial infarction ventricular tachycardia.
Determination of Niobium and Yttrium in GSJ Basalt JB‐1 by Photon Activation Analysis (1981)

New data on Nb and Y in GSJ Basalt JB‐1 obtained by photon activation analysis with 30 MeV bremsstrahlung are presented and compared with literature values.
Direct force measurements on peeling heteropolymer ssDNA from a graphite surface using single-molecule force spectroscopy (2013)

We report here a systematic investigation of the interactions between two heteropolymer DNA single-strands (ssDNA) and graphite surfaces using AFM-based single-molecule force spectroscopy (SMFS). For this purpose, force-displacement (FD) curves are recorded by peeling single-molecule ssDNA from graphite. We find that the unbinding forces are affected both by the DNA sequences and the ionic strength of the liquid environment. In particular, the unbinding force decreases with the increase of ionic strength. Dynamic force measurements indicate that the unbinding force increases nonlinearly with the logarithm of the applied loading rate. The force data at different loading rates can be fitted with a recently developed single-barrier adsorption model, which is used here as a mean of quantifying the differences in the adsorption between different sequences. In addition, we investigate the effect of DNA hybridization and the presence of mismatch pairing defects and find that flawless hybridization to a complementary oligomer significantly decreases the unbinding force but mismatched hybridization has no obvious effect on it. These results can help optimize a recently envisaged SMFS-based biosensing technology for label-free DNA detection.
Engineering large animal models of human disease (2015)

The recent development of gene editing tools and methodology for use in livestock enables the production of new animal disease models. These tools facilitate site-specific mutation of the genome, allowing animals carrying known human disease mutations to be produced. In this review, we describe the various gene editing tools and how they can be used for a range of large animal models of diseases. This genomic technology is in its infancy but the expectation is that through the use of gene editing tools we will see a dramatic increase in animal model resources available for both the study of human disease and the translation of this knowledge into the clinic. Comparative pathology will be central to the productive use of these animal models and the successful translation of new therapeutic strategies.
The erythromycin breath test as a predictor of cyclosporine blood levels (1990)

The daily dose of cyclosporine required to attain a desired blood level can vary greatly among patients. Because elimination of cyclosporine depends on its metabolism in the liver by an enzyme (cytochrome P-450IIIA) that also demethylates erythromycin, we reasoned that the ability of patients to demethylate a test dose of erythromycin might be useful in estimating their appropriate daily doses of cyclosporine. Accordingly, the [14C-N-methyl] erythromycin breath test was administered to 32 patients before they received 3.0, 5.0, or 7.5 mg/kg/day cyclosporine to treat psoriasis. We found that a simple mathematical equation incorporating just the 14CO2 production, the age of the patient, and the daily dose of cyclosporine accounted for almost 80% (R2 = 0.78) of the interpatient variability in cyclosporine blood levels we observed. Our data indicate that P-450IIIA activity largely accounts for the relationship between dose of cyclosporine and blood levels for an individual patient. We conclude that the erythromycin breath test may be a convenient guide for cyclosporine dosing.
Phase Behavior of Symmetric Sulfonated Block Copolymers (2008)

Phase behavior of poly(styrenesulfonate-methylbutylene) (PSS-PMB) block copolymers was studied by varying molecular weight, sulfonation level, and temperature. Molecular weights of the copolymers range from 2.9 to 117 kg/mol. Ordered lamellar, gyroid, hexagonally perforated lamellae, and hexagonally packed cylinder phases were observed in spite of the fact that the copolymers are nearly symmetric with PSS volume fractions between 0.45 and 0.50. The wide variety of morphologies seen in our copolymers is inconsistent with current theories on block copolymer phase behavior such as self-consistent field theory. Low molecular weight PSS-PMB copolymers (<6.2 kg/mol) show order−order and order–disorder phase transitions as a function of temperature. In contrast, the phase behavior of high molecular weight PSS-PMB copolymers (>7.7 kg/mol) is independent of temperature. Due to the large value of Flory–Huggins interaction parameter, χ, between the sulfonated and non-sulfonated blocks, PSS-PMB copolymers with PSS and PMB molecular weights of 1.8 and 1.4 kg/mol, respectively, show the presence of an ordered gyroid phase with a 2.5 nm diameter PSS network. A variety of methods are used to estimate χ between PSS and PMB chains as a function of sulfonation level. Some aspects of the observed phase behavior of PSS-PMB copolymers can be rationalized using χ.
Differences in Risk Factors for Local and Distant Recurrence After Breast-Conserving Therapy or Mastectomy for Stage I and II Breast Cancer: Pooled Results of Two Large European Randomized Trials (2001)

Age no more than 35 years and the presence of an extensive intraductal component are associated with an increased risk of local recurrence after breast-conserving therapy. Vascular invasion causes a higher risk of local recurrence after mastectomy as well as after breast-conserving therapy and should therefore not be used for deciding between the two treatments.
Impacts of US and European Financial Regulatory Reform on Japanese Real Estate Market after the Financial Crisis (2011)

概要：今回の世界金融危機の震源地となったアメリカでは，大恐慌後以来となる抜本的な金融規制改革法が2010年7月に成立した。金融市場のグローバル化に伴い，規制の潜脱を抑止する観点から，アメリカは各国に同様の措置を講じるよう要請している。欧州では既にいくつかの共通する規制強化が検討されつつあり，また，バーゼルⅢについても大枠が合意された。本稿では，欧米主要国での金融規制の強化が本邦不動産市場に与える経路と影響について考察する。
Sparse multidimensional representation using shearlets (2005)

In this paper we describe a new class of multidimensional representation systems, called shearlets. They are obtained by applying the actions of dilation, shear transformation and translation to a fixed function, and exhibit the geometric and mathematical properties, e.g., directionality, elongated shapes, scales, oscillations, recently advocated by many authors for sparse image processing applications. These systems can be studied within the framework of a generalized multiresolution analysis. This approach leads to a recursive algorithm for the implementation of these systems, that generalizes the classical cascade algorithm.
An Explosion Instrument for Disrupting Tissues and Cells (1960)

A tissue gun (Model A .22 caliber) is described which uses commercially available .22 caliber blank cartridges developed for power tools such as stud drivers and a captive piston to drive tissue through screens of various pore sizes, or through matrices of quartz, carborundum, ceramics, or other abrasive materials. The same method may be used for greater volumes, with a similar apparatus of larger dimensions. With a solid disc, instead of screens, the gun can also be used to apply high pressures of short duration to liquids or cells in suspension as a means of sterilizing them. Heat, gases, and unburned powder do not reach the tissues because of the close tolerance in the construction of the piston. No frothing or heating of the tissues takes place during disintegration. While this gun was designed primarily for use in germ-free isolators, it has much wider applicability in the laboratory. A particular advantage is that both the gun and the cartridges can be sterilized. The gun is made entirely of stainless steel and is sturdily constructed to contain the pressures developed with the cartridges recommended. It is simple to use and involves little time. Safety features have been built into the gun to prevent accidental discharge or to check the piston if an empty gun is fired.
BIOINFORMATICS IS A KEY LIFE SCIENCE R & D ACTIVITY (2009)

Rapid advances in technologies like genomic as well as bioinformatics coupled with a unique collaboration between industry and academia are beginning to show the true potential for the human genome project to affect patient healthcare. By knowing the sequence of the human genome and beginning to unravel the location and sequence of all genes and their variants, scientists can establish a better understanding of the mechanisms for diseases, with subsequent availability of new treatments. Because of the vast amount of data coming out of the Human Genome Project, bioinformatics tools and databases have become an integral part of pharmacogenomic and disease susceptibility gene research.
Efficient decoding of block turbo codes (2018)

Block turbo codes (BTCs) under iterative decoding are product codes showing excellent performance with reasonable complexity, whose component codes are conventionally decoded in two stages. The Chase algorithm is employed in the first stage to make a list of candidate codewords from the received vector, while the extrinsic information for iterative decoding is generated in the second stage. In this paper, we propose an efficient decoding algorithm for BTCs. The proposed algorithm can avoid a number of unnecessary hard-decision decoding operations by imposing two conditions on the Chase algorithm. Also, it simply computes the extrinsic information for the decision codeword. Numerical results demonstrate that the proposed algorithm has not only much lower computational complexity, but also a little better performance than the conventional decoding scheme based on the Chase algorithm. Furthermore, it can provide a trade-off between the performance and the computational complexity of BTCs by properly selecting a decoding parameter.
Advances in Polymeric Nanofiltration Membrane: A Review (2016)

The nanofiltration membrane was first introduced during late 1980s possessing properties between reverse osmosis and ultrafiltration membrane. Nanofiltration membranes have been used for applications including food industry, pharmaceutical, wastewater treatment, and desalination. This review presents an inclusive outlook of recent research and advances in polymeric nanofiltration membrane technology. Various methods were reported for nanofiltration membrane preparation particularly through electron beam irradiation, UV/photografting, layer by layer, plasma treatment, interfacial polymerization, and nanoparticle incorporation. Nanofiltration membranes were reported to remove microorganisms, turbidity, dissolved salts, and hardness. Major problem in application is nanofiltration membrane fouling, thus efforts regarding fouling mitigation are discussed.
Fluorescent Biomembrane Probe for Ratiometric Detection of Apoptosis (2007)

Herein, we developed the first ratiometric fluorescent probe for apoptosis detection. This probe incorporates selectively into the outer leaflet of the cell plasma membrane and senses the loss of the plasma membrane asymmetry occurring during the early steps of apoptosis. The high specificity to the plasma membranes was achieved by introduction into the probe of a membrane anchor, composed of a zwitterionic group and a long (dodecyl) hydrophobic tail. The fluorescence reporter of this probe is 4'-(diethylamino)-3-hydroxyflavone, which exhibits excited-state intramolecular proton transfer (ESIPT), resulting in two-band emission highly sensitive to the lipid composition of the biomembranes. Fluorescence spectroscopy, flow cytometry, and microscopy measurements show that the ratio of the two emission bands of the probe changes dramatically in response to apoptosis. This response reflects the changes in the lipid composition of the outer leaflet of the cell plasma membrane because of the exposure of the anionic phospholipids from the inner leaflet at the early steps of apoptosis. Being ratiometric, the response of the new probe can be easily quantified on an absolute scale. This allows monitoring by laser scanning confocal microscopy the degree and spatial distribution of the apoptotic changes at the cell plasma membranes, a feature that can be hardly achieved with the commonly used fluorescently labeled annexin V assay.