gebhart/patrepeval huggingface dataset:
Energy Levels Calculations of 20Ne and 21Ne Isotopes (2015)

In this article by using OXBASH shell model code the energy levels of Neon isotopes 20Ne and 21Ne are calculated. This code which is based on one of the most applicable nuclear models, deals with evaluating energy levels. Applying the program for each isotope using the defined codes, introduces several files which each file contains a set of data. Meanwhile, the ground state of excitation energy evaluated by OXBASH code together with energy levels and also probable places for nucleons’ placements in each energy level. Programs will be reliable only when results meet experimental procedures. A compilation of SD-shell energy levels calculated with the USD Hamiltonian and has been published around 1988. A comparison had been made between our results and the available experimental data to test theoretical shell model description of nuclear structure in Neon isotopes. The calculated energy spectrum is in good agreement with the available experimental data.
Characterization of MEK1 phosphorylation by the v-Mos protein. (1995)

Activation of MAP kinase/Erk Kinase (MEK) via direct phosphorylation by Mos may be crucial for cellular transformation by the activated c-mos or v-mos gene. Recent studies on a number of different protein kinases showed that phosphorylation within a subdomain of the catalytic domain may represent a common mode of activation. In this regard, activation of MEK1 by Raf involves phosphorylation of serine residues 218 and 222. Here we show that recombinant kinase-inactive MEK1 is phosphorylated by v-Mos with equal efficiency at both Ser 218 and Ser 222 in vitro. Tryptic phosphopeptide analysis of glutathione-S-transferase (GST)-MEK1 K97R and its alanine-for-serine mutants indicated that Ser 222 is the preferred phosphorylation site. Wild-type GST-MEK1 was phosphorylated at the same sites but contained a significantly lower amount of doubly phosphorylated species then its K97R kinase-inactive mutant. The ratio of GST-MEK1 species phosphorylated at two serines to those phosphorylated at one serine was similar in auto-phosphorylated and v-Mos-phosphorylated GST-MEK1. Consistent with the in vitro data, phosphopeptide mapping of MEK1 immunoprecipitated from mos transformed cells showed an increased amount of singly phosphorylated phosphopeptide compared to nontransformed cels. MEK1 was found to be more highly activated in NIH3T3 cells transformed by an activated c-mos or v-mos gene than in cells growing normally in medium containing serum. Our data indicate that Mos activated MEK1 in vitro as well as in vivo by phosphorylating Ser 222.
Biocompatible Nanocarrier Fortified with a Dipyridinium-Based Amphiphile for Eradication of Biofilm (2014)

Annihilation of bacterial biofilms is challenging owing to their formidable resistance to therapeutic antibiotics and thus there is a constant demand for development of potent antibiofilm agents that can abolish established biofilms. In the present study, the activity of a dipyridinium-based cationic amphiphile (compound 1) against established bacterial biofilms and the subsequent development of a compound 1-loaded nanocarrier for potential antibiofilm therapy are highlighted. Solution-based assays and microscopic analysis revealed the antagonistic effect of compound 1 on biofilms formed by Staphylococcus aureus MTCC 96 and Pseudomonas aeruginosa MTCC 2488. In combination studies, compound 1 could efficiently potentiate the action of tobramycin and gentamicin on P. aeruginosa and S. aureus biofilm, respectively. A human serum albumin (HSA)-based nanocarrier loaded with compound 1 was generated, which exhibited sustained release of compound 1 at physiological pH. The compound 1-loaded HSA nanocarrier (C1-HNC) displayed the signature membrane-directed activity of the amphiphile on target bacteria, efficiently eliminated established bacterial biofilms, and was observed to be nontoxic to a model human cell line. Interestingly, compound 1 as well as the amphiphile-loaded HSA nanocarrier could eradicate established S. aureus biofilm from the surface of a Foley's urinary catheter. On the basis of its biocompatibility and high antibiofilm activity, it is conceived that the amphiphile-loaded nanocarrier may hold potential in antibiofilm therapy.
Characterization of three terpenoid glycosyltransferase genes in ‘Valencia’ sweet orange (Citrus sinensis L. Osbeck) (2010)

Three putative terpenoid UDP-glycosyltransferase (UGT) genes, designated CsUGT1, CsUGT2, and CsUGT3, were isolated and characterized in 'Valencia' sweet orange (Citrus sinensis L. Osbeck). CsUGT1 consisted of 1493 nucleotides with an open reading frame encoding 492 amino acids, CsUGT2 consisted of 1727 nucleotides encoding 504 amino acids, and CsUGT3 consisted of 1705 nucleotides encoding 468 amino acids. CsUGT3 had a 145 bp intron at 730-874, whereas CsUGT1 and CsUGT2 had none. The three deduced glycosyltransferase proteins had a highly conserved plant secondary product glycosyltransferase motif in the C terminus. Phylogenetic analysis showed that CsUGT1 and CsUGT3 were classified into group L of glycosyltransferase family 1, and CsUGT2 was classified into group D. Through Southern blotting analysis, CsUGT1 was found to have two copies in the sweet orange genome, whereas CsUGT2 and CsUGT3 had at least seven and nine copies, respectively. CsUGT1, CsUGT2, and CsUGT3 were constitutively expressed in leaf, flower, and fruit tissues. The results facilitate further investigation of the function of terpenoid glycosyltransferases in citrus and the biosynthesis of terpenoid glycosides in vitro.
Fast ions and hot electrons in the laser–plasma interaction (1986)

Data on the emission of energetic ions produced in laser–matter interactions have been analyzed for a wide variety of laser wavelengths, energies, and pulse lengths. Strong correlation has been found between the bulk energy per AMU for fast ions measured by charge cups and the x-ray-determined hot electron temperature. Five theoretical models have been used to explain this correlation. The models include (1) a steady-state spherically symmetric fluid model with classical electron heat conduction, (2) a steady-state spherically symmetric fluid model with flux limited electron heat conduction, (3) a simple analytic model of an isothermal rarefaction followed by a free expansion, (4) the lasnex hydrodynamics code [Comments Plasma Phys. Controlled Fusion 2, 85 (1975)], calculations employing a spherical expansion and simple initial conditions, and (5) the lasnex code with its full array of absorption, transport, and emission physics. The results obtained with these models are in good agreement with the experiments and indicate that the detailed shape of the correlation curve between mean fast ion energy and hot electron temperature is due to target surface impurities at the higher temperatures (higher laser intensities) and to the expansion of bulk target material at the lower temperatures (lower laser intensities).
An Algorithm of hidden Surface Removal based on Frame-To- Frame Coherence (1991)

Frame-to-frame coherence capitalizes on the continuity existing between successive frames in order to predict the visibility of the scene at a given instant on the basis of its visibility at the previous instant. It is shown that all the algorithms based on frame-to-frame coherence share a common model and involve similar data structures. This model is used as a framework for a discussion of possible frame-to-frame coherence algorithms. A specific solution based on a partition of the image space into several 2-D regions is then presented. A temporal graph of the depth priority relationship of the objects is first computed in a pre-process along with a temporal BSP tree of each object. In the first frame a total traversal of both data structures is required in order to establish the priority list of the faces of the scenes. In successive frames, the priority list is easily updated with partial traversals and with no geometrical computations. The complexity of the proposed algorithm is discussed. Some examples are presented with comments on the results of their implementation.
Creating Class I MHC–Null Pigs Using Guide RNA and the Cas9 Endonuclease (2014)

Pigs are emerging as important large animal models for biomedical research, and they may represent a source of organs for xenotransplantation. The MHC is pivotal to the function of the immune system in health and disease, and it is particularly important in infection and transplant rejection. Pigs deficient in class I MHC could serve as important reagents to study viral immunity as well as allograft and xenograft rejection. In this study, we report the creation and characterization of class I MHC knockout pigs using the Cas9 nuclease and guide RNAs. Pig fetal fibroblasts were genetically engineered using Cas9 and guide RNAs, and class I MHC(-) cells were then used as nuclear donors for somatic cell nuclear transfer. We produced three piglets devoid of all cell surface class I proteins. Although these animals have reduced levels of CD4(-)CD8(+) T cells in peripheral blood, the pigs appear healthy and are developing normally. These pigs are a promising reagent for immunological research.
A CMOS image sensor for high-speed imaging (2000)

Acquisition of the images of fast-moving objects requires imagers with high photoresponsivity at short integration times, synchronous exposure, and high-speed parallel readout. Previous CMOS implementations yield frame rates around 500 frames/s at integration times ranging from 75 to 200 ps, and some use rolling shutter only. This CMOS imager achieves more than 1000 frames/s with integration time in synchronous exposure variable between 1 /spl mu/s and 150 /spl mu/s. The 256/spl times/256 pixel imager is realized in a single-poly double-metal n-well 1 /spl mu/m CMOS technology.
Computational investigation of experimental interaction impedance obtained by perturbation for helical traveling-wave tube structures (1998)

Conventional methods used to measure the cold-test interaction impedance of helical slow-wave structures involve perturbing a helical circuit with a cylindrical dielectric rod placed on the central axis of the circuit. It has been shown that the difference in resonant frequency or axial phase shift between the perturbed and unperturbed circuits can be related to the interaction impedance. However, because of the complex configuration of the helical circuit, deriving this relationship involves several approximations. With the advent of accurate three-dimensional (3-D) helical circuit models, these standard approximations can be fully investigated. This paper addresses the most prominent approximations made in the analysis for measured interaction impedance by Lagerstrom (1957) and investigates their accuracy using the 3-D simulation code MAFIA. It is shown that a more accurate value of interaction impedance can be obtained by using 3-D computational methods rather than performing costly and time consuming experimental cold-test measurements.
A Single Na + Channel Mutation Causing Both Long-QT and Brugada Syndromes (1999)

Mutations in SCN5A, the gene encoding the cardiac Na(+) channel, have been identified in 2 distinct diseases associated with sudden death: one form of the long-QT syndrome (LQT(3)) and the Brugada syndrome. We have screened SCN5A in a large 8-generation kindred characterized by a high incidence of nocturnal sudden death, and QT-interval prolongation and the "Brugada ECG" occurring in the same subjects. An insertion of 3 nucleotides (TGA) at position 5537, predicted to cause an insertion of aspartic acid (1795insD) in the C-terminal domain of the protein, was linked to the phenotype and was identified in all electrocardiographically affected family members. ECGs were obtained from 79 adults with a defined genetic status (carriers, n=43; noncarriers, n=36). In affected individuals, PR and QRS durations and QT intervals are prolonged (P<0.0001 for all parameters). ST segment elevation in the right precordial leads is present as well (P<0.0001). Twenty-five family members died suddenly, 16 of them during the night. Expression of wild-type and mutant Na(+) channels in Xenopus oocytes revealed that the 1795insD mutation gives rise to a 7.3-mV negative shift of the steady-state inactivation curve and an 8.1-mV positive shift of the steady-state activation curve. The functional consequence of both shifts is likely to be a reduced Na(+) current during the upstroke of the action potential. LQT(3) and Brugada syndrome are allelic disorders but may also share a common genotype.
Carbohydrate Biopolymers Enhance Antibody Responses to Mucosally Delivered Vaccine Antigens (2000)

We have evaluated the ability of two carbohydrate biopolymers, chitosan and gellan, to enhance antibody responses to subunit influenza virus vaccines delivered to the respiratory tracts of mice. Groups of mice were vaccinated three times intranasally (i.n.) with 10 microg of purified influenza B/Panama virus surface antigens (PSAs), which consist of hemagglutinin (HA) and neuraminidase (NA), either alone or admixed with chitosan or gellan solutions. Separate groups were vaccinated subcutaneously (s.c.) with PSAs adsorbed to Alhydrogel or chitosan or gellan alone i.n. Serum antibody responses were determined by enzyme-linked immunosorbent assay (ELISA) for influenza virus-specific immunoglobulin G (IgG) and by HA inhibition (HAI) and NA inhibition (NAI) assays. The local respiratory immune response was measured by assaying for influenza virus-specific IgA antibody in nasal secretions and by enumerating nasal and pulmonary lymphocytes secreting IgA, IgG, and IgM anti-influenza virus-specific antibodies by enzyme-linked immunospotting (ELISPOT). When administered alone i.n., B/Panama PSA was poorly immunogenic. Parenteral immunization with B/Panama PSA with Alhydrogel elicited high titers of anti-B/Panama antibodies in serum but a very poor respiratory anti-B/Panama IgA response. In contrast, i.n. immunization with PSA plus chitosan stimulated very strong local and systemic anti-B/Panama responses. Gellan also enhanced the local and serum antibody responses to i.n. PSA but not to the same extent as chitosan. The ability of chitosan to augment the immunogenicity of influenza vaccines given i.n. was confirmed using PSA prepared from an influenza A virus (A/Texas H1N1).
A STUDY OF TECHNIQUES FOR THE EXAMINATION OF SPUTUM IN A FIELD SURVEY OF CHRONIC BRONCHITIS. (1963)

By the time patients with established chronic bronchitis seek advice for their disability, events associated with the development of their first symptoms have usually been forgotten (1). Field studies are necessary, therefore, to observe the early natural history of the disease. For this purpose, simple, valid, and reproducible diagnostic methods are needed, including symptomatic questionnaires, respiratory function tests, and sputum examinations. The use of these methods in field surveys of chronic bronchitis has been studied in considerable detail (2-4) and their value in population prevalence studies demonstrated (5-8). This paper reports further studies of techniques for examining the cellular content of sputum suitable for epidemiologic work. The work, which was undertaken during the early stages of a long-term prospective study of chronic bronchitis, will be described in two parts. First, a simple scheme for the visual grading of sputum purulence was developed and the relation of the grades to cell count was examined. Second, a rapid quantitative method for detecting sputum eosinophilia was tested, and the prevalence and significance of this finding was studied.
Scheduled Sampling for Sequence Prediction with Recurrent Neural Networks (2015)

Recurrent Neural Networks can be trained to produce sequences of tokens given some input, as exemplified by recent results in machine translation and image captioning. The current approach to training them consists of maximizing the likelihood of each token in the sequence given the current (recurrent) state and the previous token. At inference, the unknown previous token is then replaced by a token generated by the model itself. This discrepancy between training and inference can yield errors that can accumulate quickly along the generated sequence. We propose a curriculum learning strategy to gently change the training process from a fully guided scheme using the true previous token, towards a less guided scheme which mostly uses the generated token instead. Experiments on several sequence prediction tasks show that this approach yields significant improvements. Moreover, it was used successfully in our winning entry to the MSCOCO image captioning challenge, 2015.
Characterization of the Interaction of Natural Proline-Rich Peptides with Five Different SH3 Domains (1994)

The interaction of six different proline-rich peptides with five SH3 domains has been investigated by using spectroscopic techniques. These peptides correspond to natural sequences and have been implicated in the interaction of some SH3 domains with other proteins. We have determined the Kd values for all of the possible combinations between the peptides and the SH3 domains. Low specificity and low affinity (> 5 microM) are the most remarkable conclusions from these studies. None of the peptides tested here were found to bind with significant affinity to spectrin-SH3 or n-src-SH3. Abl-SH3 seems to be the most selective of the domains analyzed here, while Fyn-SH3 is the most promiscuous. CD and FTIR studies indicate that these peptides adopt to different extents a PPII-like structure in aqueous solution. However, analysis of the SH3 domain complexes with these peptides suggests that proline-rich peptides do not necessarily adopt an overall PPII structure over their entire length upon binding to the different SH3 domains.
Synthesis of Speaker Facial Movement to Match Selected Speech Sequences (1994)

A system is described which allows for the synthesis of a video sequence of a realistic-appearing talking human head. A phonic based approach is used to describe facial motion; image processing rather than physical modeling techniques are used to create video frames.
Hardware authentication based on PUFs and SHA-3 2<sup>nd</sup> round candidates (2010)

Security features are getting a growing interest in microelectronics. Not only entities have to authenticate in the context of a high secure communication but also the hardware employed has to be trusted. Silicon Physical Unclonable Functions (PUFs) or Physical Random Functions, which exploits manufacturing process variations in integrated circuits, have been used to authenticate the hardware in which they are included and, based on them, several cryptographic protocols have been reported. This paper describes the hardware implementation of a symmetric-key authentication protocol in which a PUF is one of the relevant blocks. The second relevant block is a SHA-3 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">nd</sup> round candidate, a Secure Hash Algorithm (in particular Keccak), which has been proposed to replace the SHA-2 functions that have been broken no long time ago. Implementation details are discussed in the case of Xilinx FPGAs.
A liquid chromatography/electrospray mass spectrometric study on the post-transcriptional modification of tRNA (1998)

Liquid chromatography/electrospray mass spectrometry is one of the rapidly developing techniques with which mass of large hydrophilic polymers such as proteins and nucleic acids can be determined precisely. The technique was applied to studies on the modifications of tRNAs. Various tRNA species purified from Escherichia coli were directly injected into a capillary reversed-phase column and the desalted and concentrated tRNAs were analyzed on-line with an electrospray mass spectrometer. In some cases, small but significant differences were noted between the theoretical and observed molecular masses, suggesting that there exist still unknown modifications. Under high resolution measurements, multiple peaks corresponding to species modified to a varying extent were resolved. To study the structures in detail, the isolated tRNA species were digested with ribonuclease T1, and the resulting mixture of fragments were analyzed by the same liquid chromatography/mass spectrometry. In this way, most of the fragments were easily identified solely from their masses, and the positions where the expected and real structures differ were revealed. The results obtained showed the presence of micro-heterogeneity among tRNAs and demonstrated at the same time the power of the hyphenated technique for the structural analysis on nucleic acids.
Psychosocial and Behavioral Aspects of Bariatric Surgery (2005)

Bariatric surgery has become an increasingly popular treatment option for individuals with extreme obesity (defined as a BMI > or = 40 kg/m2) or those with less severe obesity accompanied by significant comorbidities. Sustained postoperative weight loss and improvements in obesity-related health problems make bariatric surgery the most effective treatment for this population. Nevertheless, most experts agree that psychosocial and behavioral factors contribute to successful postoperative outcomes. This paper reviews the literature on the preoperative psychosocial status, eating behaviors, and quality of life of patients who seek bariatric surgery. In addition, the paper examines studies that investigated changes in these factors postoperatively. The review concludes with an agenda for future research in this area.
Novel Ablation Catheter Technology that Improves Mapping Resolution and Monitoring of Lesion Maturation (2012)

We hypothesized that adding pin electrodes (PEs) near the ablation tip enhances the assessment of electrical activity and lesion efficacy using electrogram amplitudes (Amp) and maximum frequency spectra (Maxfreq). We used an 8-mm ablation catheter equipped with 461mm PEs radially distributed at 90 u and standard recording rings. Lesions were placed under fluoroscopic and St. Jude NavX guidance to form intercaval (IC), cavotricuspid isthmus (CTI) lines and left atrial linear lesions (LL). Radiofrequency (RF) was delivered for 1 min at settings of 65 u C and 65 watts. Amp and MaxFreq were recorded pre-and post ablation from bipolar PEs, PEs referenced to the 8 mm tip and 8 mm to the first ring electrode. Linear lesion gaps and atrial tachycardia were mapped and ablated using PE recordings. Post-mortem tetrazolium staining of RF lesion assessment was performed. In seven dogs and 217 lesions, Amp showed marked decreases post ablation when measured with the PE compared to the 8-mm tip (77.317.9% decrease versus 27.338.9%, p,0.0001). Using the PE, the MaxFreq decreased significantly compared with the 8mm tip 5622.9% versus 11.436.5, p,0.001). Gaps and atrial tachycardia-induced post LL lesions were ablated based on PE electrical activity, indicating gaps and viable tissue. Such discrimination was not possible with the 8-mm electrode. PEs show more dramatic changes in Amp and MaxFreq versus the standard 8-mm tip. The PE enhances the detection of gaps in the linear lesion. We conclude that PEs offer significant improvement in the assessment of RF lesion efficacy and provide a useful index of lesion formation and post-ablation lesion mapping and gap detection.