Miracle-dz/UniFAR-FTUs huggingface dataset:
Towards the Generation of Artificial O6‐Alkylguanine‐DNA Alkyltransferases: In Vitro Selection of Antibodies with Reactive Cysteine Residues

A stepwise approach to the development of artificial O6-alkylguanine-DNA alkyltransferases (AGTs) and its application to the in vitro selection of antibodies with highly reactive cysteine residues are described. As a result of low reactivity of O6-alkylated guanine as a substrate in SN2 reactions, a stepwise selection of artificial AGTs in which sulfuhydryl-specific reagents of the types II and III are first used to generate antibodies with reactive cysteine residues is ideal. These antibodies are then the basis for selections against O6-alkylguanine derivs. of the type I. To evaluate whether the selected antibodies possess reactive cysteine residues, the gp3 gene, which anchors the antigen-binding fragment (Fab) on the phage, was deleted from the phagemids and crude exts. of Escherichia coli XL1-Blue that expressed Fab were analyzed. For the construction of the single-chain format RD3 (scRD3) antibody from the two variable domains, the orientation of light variable domain (VL)-linker-heavy variable domain (VH) was selected, with a nonrepetitive peptide of 20 amino acids as a linker. The scRD3 antibody possesses two unpaired cysteine residues with considerably different reactivity. Anal. of the reaction of the Fab RD3 antibody with III revealed that the RD3 clone also possesses two cysteine residues with differing reactivity. [on SciFinder (R)]
In vitro elution of amikacin and vancomycin from impregnated plaster of Paris beads.

OBJECTIVE To describe in vitro elution characteristics of amikacin and vancomycin from calcium sulfate hemihydrate 98% (plaster of Paris, POP) beads and characterize eluent inhibition of Staphylococcus spp. STUDY DESIGN Experimental study. METHODS POP beads were impregnated with amikacin or vancomycin alone or in combination and then incubated alone or in combination for 84 days at 37 degrees C in plastic tubes containing sterile phosphate-buffered saline (PBS). Beads containing no antimicrobial served as negative control. Beads were intermittently moved to a new tube containing drug-free PBS. Antimicrobial was measured in the eluent using a polarized fluorescent immunoassay. Eluent inhibition of Staphylococcus spp. was determined at each time point. RESULTS Antimicrobial release from beads was characterized by an initial rapid phase then a slower phase. Although antimicrobial release from beads occurred throughout the 84 days, most was in the first 24 hours, except for vancomycin alone. Duration of eluent inhibition of Staphylococcus spp. growth ranged from 0.5 (amikacin alone) to 56 days (vancomycin alone). Control eluent did not inhibit bacterial growth. CONCLUSIONS Amikacin elution from POP beads was rapid, inhibiting growth for <24 hours with or without vancomycin. Vancomycin elution was slower and inhibited growth for 56 days alone or for 5 days with amikacin. CLINICAL RELEVANCE Vancomycin-impregnated beads appear to be reasonable as a therapeutic option whereas amikacin-impregnated POP beads and amikacin and vancomycin combinations may require further study before considering as a therapeutic option.
Geographic, farm, and animal factors associated with multiple antimicrobial resistance in fecal Escherichia coli isolates from cattle in the western United States.

OBJECTIVE To describe geographic, farm-type, and animal-type factors associated with multiple antimicrobial resistance (MAR) in fecal Escherichia coli isolates from cattle. DESIGN Cross-sectional field study. SAMPLE POPULATION 1,736 fecal samples from cattle on 38 farms in California, Oregon, and Washington. PROCEDURES Fecal samples were collected from preweaned calves (2 to 4 weeks old) and cows that recently calved on dairy and beef cow-calf farms, preweaned calves on calf ranches, and 1-year-old steers on feedlots. One fecal E coli isolate per sample was isolated, and antimicrobial susceptibility was tested. Escherichia coli isolates were initially clustered by antimicrobial resistance patterns and categorized by number of antimicrobial resistances. A generalized estimating equations cumulative logistic regression model was used to identify factors associated with an increase in MAR in fecal E coli isolates from cattle. RESULTS MAR was higher in E coli isolates from cattle in California, compared with those from cattle in Washington or Oregon. Multiple antimicrobial resistance was highest in E coli isolates from calves on calf ranches and progressively lower in isolates from feedlot steers, dairy cattle, and beef cattle. Multiple antimicrobial resistance was higher in E coli isolates from calves than from adult cattle, in E coli isolates from cattle of conventional farms than of organic farms, and in isolates from beef cattle in intensive dairy farm regions than from beef cattle distant from dairy farm regions. CONCLUSIONS AND CLINICAL RELEVANCE MAR in fecal E coli isolates from cattle was influenced by factors not directly associated with the use of antimicrobials, including geographic region, animal age, and purpose (beef vs dairy).
The Impact of the Pull of the Recent on the History of Marine Diversity

Up to 50% of the increase in marine animal biodiversity through the Cenozoic at the genus level has been attributed to a sampling bias termed “the Pull of the Recent,” the extension of stratigraphic ranges of fossil taxa by the relatively complete sampling of the Recent biota. However, 906 of 958 living genera and subgenera of bivalve mollusks having a fossil record occur in the Pliocene or Pleistocene. The Pull of the Recent thus accounts for only 5% of the Cenozoic increase in bivalve diversity, a major component of the marine record, suggesting that the diversity increase is likely to be a genuine biological pattern.
Contact Active Antimicrobial Coatings Prepared by Polymer Blending.

Herein, contact active antimicrobial films are prepared by simply blending cationic amphiphilic block copolymers with commercial polystyrene (PS). The copolymers are prepared by combining atom transfer radical polymerization and "click chemistry. " A variety of copolymers are synthesized, and composed of a PS segment and an antimicrobial block bearing flexible side chain with thiazole and triazole groups, 4-(1-(2-(4-methylthiazol-5-yl)ethyl)-1H-1,2,3-triazol-4-yl) butyl methacrylate (TTBM). The length of the TTBM block is varied as well as the alkylating agent. Different films are prepared from N,N-dimethylformamide solution, containing variable PS-b-PTTBM/PS ratio: from 0 to 100 wt%. Remarkably, the blend films, especially those with 30 and 50 wt% of copolymers, exhibit excellent antimicrobial activities against Gram-positive, Gram-negative bacteria and fungi, even higher than films prepared exclusively from the cationic copolymers. Blends composed of 50 wt% of the copolymers present a more than 99.999% killing efficiency against the studied microorganisms. The better activity found in blends can be due to the higher roughness, which increases the surface area and consequently the contact with the microorganisms. These results demonstrate that the use of blends implies a reduction of the content of antimicrobial agent and also enhances the antimicrobial activity, providing new insights for the better designing of antimicrobial coatings.
HLA‐A*0201 presents TAP‐dependent peptide epitopes to cytotoxic T lymphocytes in the absence of tapasin

Tapasin is a 48‐kDa endoplasmic reticulum (ER)‐resident glycoprotein that binds to the transporter associated with antigen processing (TAP) and mediates an interaction between TAP and newly synthesized MHC class I molecules. It is also essential for the proper antigen presenting function of HLA‐A*0101 (HLA‐A1), HLA‐A*0801 (HLA‐B8) and HLA‐B*4402 (HLA‐B4402). We show here that while tapasin is required for HLA‐A*0201 (HLA‐A2) molecules to bind to TAP, its absence does not block the presentation of HLA‐A2‐restricted TAP‐dependent epitopes to cytotoxic T lymphocytes indicating that, unlike HLA‐A1, HLA‐B8 and HLA‐B4402, HLA‐A2 has access to the TAP‐dependent peptide pool even in the absence of tapasin. Nevertheless, the overall efficiency with which HLA‐A2 was loaded with optimal, stabilizing peptides was impaired in the cell line . 220, resulting in a significant increase in the fraction of HLA‐A2 molecules being released from the ER in a “peptide‐receptive” state.
Influence of metal ions on pellet morphology and polygalacturonase synthesis by Aspergillus niger 3T5B8

O efeito da adicao de cations na morfologia do agregado e na sintese de poligalacturonase (PG) por Aspergillus niger 3T5B8 foi estudado e comparado com um sistema controle. Fe(II), Cu(II), Zn(II) and Mn(II) foram adicionados ao meio de fermentacao, tanto separadamente, como em grupos de cations. A adicao dos ions Fe2+ e/ou Zn2+ foi positivamente significante para a producao da enzima. Um efeito similar no teor de biomassa, contudo, so pode ser observado quando os mesmos ions foram adicionados isoladamente. Por outro lado, os ions Cu2+ e Mn2+ nao afetaram significativamente estes parâmetros. Utilizando-se tecnicas de processamento de imagens para o estudo da morfologia dos pellets, observou-se que pequenos aglomerados, com pequenos nucleos, foram geralmente obtidos quando os cations Fe2+ e Zn2+ foram adicionados ao meio, seja isolada ou simultaneamente. Os aglomerados produzidos em meios contendo ions Fe2+ ou Zn2+ eram compactos, enquanto que aqueles produzidos em meios contendo ambos os cations foram considerados difusos. A autolise do nucleo foi observada para os grandes agregados produzidos no meio controle, devido ao transporte deficiente de nutrientes para o seu interior. Os agregados produzidos em meio contendo os ions Fe2+ e Zn2+ foram grandes produtores de enzima, provavelmente devido a uma morfologia mais "frouxa", induzida pela presenca combinada destes metais no meio, favorecendo o transporte de nutrientes.
The analysis of relation between Q-factor and phase noise by using substrate-integrated waveguide cavity oscillators

The relation between Q-factor and phase noise is verified in this paper. According to the phase noise model proposed by D.B. Leeson in 1966, it estimates about a 6 dB reduction in phase noise as Q-value of resonator doubled. By fabricating three substrate-integrated waveguide cavity oscillators on different substrates with different Q-values, we could obtain the same tendencies between measurements and computed values from the proposed model and thus verified the relation between Q-factor and phase noise.
Comparative Analysis of 22 Coronavirus HKU1 Genomes Reveals a Novel Genotype and Evidence of Natural Recombination in Coronavirus HKU1

ABSTRACT We sequenced and compared the complete genomes of 22 strains of coronavirus HKU1 (CoV HKU1) obtained from nasopharyngeal aspirates of patients with respiratory tract infections over a 2-year period. Phylogenetic analysis of 24 putative proteins and polypeptides showed that the 22 CoV HKU1 strains fell into three clusters (genotype A, 13 strains; genotype B, 3 strains and genotype C, 6 strains). However, different phylogenetic relationships among the three clusters were observed in different regions of their genomes. From nsp4 to nsp6, the genotype A strains were clustered with the genotype B strains. For nsp7 and nsp8 and from nsp10 to nsp16, the genotype A strains were clustered with the genotype C strains. From hemagglutinin esterase (HE) to nucleocapsid (N), the genotype B strains were clustered closely with the genotype C strains. Bootscan analysis showed possible recombination between genotypes B and C from nucleotide positions 11500 to 13000, corresponding to the nsp6-nsp7 junction, giving rise to genotype A, and between genotypes A and B from nucleotide positions 21500 to 22500, corresponding to the nsp16-HE junction, giving rise to genotype C. Multiple alignments further narrowed the sites of crossover to a 143-bp region between nucleotide positions 11750 and 11892 and a 29-bp region between nucleotide positions 21502 and 21530. Genome analysis also revealed various numbers of tandem copies of a perfect 30-base acidic tandem repeat (ATR) which encodes NDDEDVVTGD and various numbers and sequences of imperfect repeats in the N terminus of nsp3 inside the acidic domain upstream of papain-like protease 1 among the 22 genomes. All 10 CoV HKU1 strains with incomplete imperfect repeats (1.4 and 4.4) belonged to genotype A. The present study represents the first evidence for natural recombination in coronavirus associated with human infection. Analysis of a single gene is not sufficient for the genotyping of CoV HKU1 strains but requires amplification and sequencing of at least two gene loci, one from nsp10 to nsp16 (e.g., pol or helicase) and another from HE to N (e.g., spike or N). Further studies will delineate whether the ATR is useful for the molecular typing of CoV HKU1.
Spectral element methods on triangles and quadrilaterals : comparisons and applications

In this paper, we compare a triangle based spectral element method (SEM) with the classical quadrangle based SEM and with a standard spectral method. For the sake of completeness, the triangle-SEM, making use of the Fekete points of the triangle, is first revisited. The requirement of a highly accurate quadrature rule is particularly emphasized. Then it is shown that the convergence properties of the triangle-SEM compare well with those of the classical SEM, by solving an elliptic equation with smooth (but steep) analytical solution. It is also proved numerically that the condition number grows significantly faster for triangles than for quadrilaterals. Finally, the attention is focused on a diffraction problem to show the high flexibility of the triangle-SEM. 2004 Elsevier Inc. All rights reserved. PACS: 65N30; 65M60; 65M70
Survey of approaches for assessing software energy consumption

Though the energy consumption of software-controlled ICT systems ranging from mobile devices to data centers is increasingly gaining attention, energy optimization is still far from an established task in the software development process. Therefore, we have surveyed the available research on assessing the energy consumption of software systems, which showed a lack of development tools, but several approaches exist for measuring the energy consumption. We group these approaches according to how measurement data is made available and compare several characteristics of the collected data. The survey shows that not only development tools for software energy optimization are still missing, but there is also a lack of fine-grained measurement approaches as well as approaches for general-purpose platforms.
Electro-optic high voltage sensor for utility application

Recently, optical sensors for current and voltage measurement in electric transmission grids have attracted increased interest. In comparison to conventional instrument transformers they benefit from being smaller and lighter at reduced cost, easy integration into digital substations, enhanced performance (bandwidth of several 100 kHz; no saturation), and inherent dielectric decoupling of the sensor electronics. State-of-the-art current sensors typically use the Faraday effect in an optical fiber wrapped around the high voltage current conductor in a closed loop [1]. Voltage sensors are often based on the linear electro-optic effect (Pockels effect) in relatively short (<;20 cm) crystals. At voltages of several 100 kV, the resulting high electric field strengths require rather complex and expensive dielectric insulation, e.g. with pressurized SF6-gas [2].
Common structural features in gramicidin and other ion channels

This review compares and contrasts the structures of several different types of ion channels with known three‐dimensional structures, including gramicidin and the family of peptaibol channels, as well as the Streptomyces lividans potassium channel, to reveal common features in their structures that relate to their functional roles in ion binding and transport across membranes. Specifically, the locations of aromatic amino acids, the dimensions of the molecules, the multimeric nature of the channels and the roles of hydrogen bonds in stabilising such structures, the means by which the channels open and close, and the chemical nature of the groups which make up the channel lumen are discussed. The emphasis is on the commonality of features found in model channels, which may ultimately be found in other biological channel structures. BioEssays 22:227–234, 2000. © 2000 John Wiley & Sons, Inc.
The involvement of spinal bovine adrenal medulla 22‐like peptide, the proenkephalin derivative, in modulation of nociceptive processing

Bovine adrenal medulla 22 (BAM22), one of the cleavage products of proenkephalin A, possesses high affinity for opioid receptors and sensory neuron‐specific receptor (SNSR). The present study was designed to examine the expression of BAM22 in the spinal cord and dorsal root ganglion (DRG) of naive rats as well as in a model of inflammation. BAM22‐like immunoreactivity (BAM22‐IR) was expressed in fibers in the spinal cord, with high density seen in lamina I in naïve rats. The expression of BAM22‐IR in the superficial laminae was greatly reduced following dorsal rhizotomy. BAM22‐IR was also located in 19% of DRG cells, mainly in the small‐ and medium‐sized subpopulations. Following injection of complete Freund's adjuvant (CFA) in the hindpaw, the expression of BAM22‐IR in the superficial laminae of the spinal cord and small‐sized DRG neurons on the ipsilateral side was markedly increased. Double labeling showed that the Fos‐positive nucleus was surrounded by BAM22‐IR cytoplasm in the spinal dorsal horn neurons or closely associated with BAM22‐IR fibers in the superficial laminae. Furthermore, CFA‐induced mechanical allodynia in the inflamed paw was potentiated by intrathecal administration of anti‐BAM22 antibody. Together, these results demonstrate for the first time that BAM22‐like peptide is mainly located in the superficial laminae of the spinal cord and mostly originates from nociceptive DRG neurons. BAM22 could thus act as a ligand for presynaptic opioid receptors and SNSR. Our study also provides evidence suggesting that BAM22 plays a role in the modulation of nociceptive processing at the spinal level under normal and inflammatory conditions.
ANNP: a neural network parser for real world texts

A neural parser is described that computes sentence structure and achieves compositionality in a simple and effective way. The model is compositional in the sense that it is able to analyze new structures which are recursive combinations of known structures. The model's performance is compared to a recently proposed neural parser in terms of efficiency and computational capacity. To test the efficiency of the model we ran two groups of experiments. In the first group, we used the same training and test sentences as did Mikkulainen (1996). In the second group of experiments, we used real texts and integrated the parser with a syntactic disambiguation system as well as a semantic disambiguation system. The objective of the second group of experiments was to maximize the compositionality; from the simplest training set possible, the maximum number of complex sentences could be analyzed in the test phase. The results obtained are very promising.
A first order approximation to the optimum checkpoint interval

To avoid having to restart a job from the beginning in case of random failure, it is standard practice to save periodically sufficient information to enable the job to be restarted at the previous point at which information was saved. Such points are referred to as checkpoints, and the saving of such information at these points is called checkpointing [1].
Antisense RNA directed against the 3' noncoding region prevents dormant mRNA activation in mouse oocytes.

Primary mouse oocytes contain untranslated stable messenger RNA for tissue plasminogen activator (t-PA). During meiotic maturation, this maternal mRNA undergoes a 3'-polyadenylation, is translated, and is degraded. Injections of maturing oocytes with different antisense RNA's complementary to both coding and noncoding portions of t-PA mRNA all selectively blocked t-PA synthesis. RNA blot analysis of t-PA mRNA in injected, matured oocytes suggested a cleavage of the RNA.RNA hybrid region, yielding a stable 5' portion, and an unstable 3' portion. In primary oocytes, the 3' noncoding region was susceptible to cleavage, while the other portions of the mRNA were blocked from hybrid formation until maturation occurred. Injection of antisense RNA complementary to 103 nucleotides of its extreme 3' untranslated region was sufficient to prevent the polyadenylation, translational activation, and destabilization of t-PA mRNA. These results demonstrate a critical role for the 3' noncoding region of a dormant mRNA in its translational recruitment during meiotic maturation of mouse oocytes.
Conjoint Analysis for Mobile Devices for Ubiquitous Learning in Higher Education: The Korean Case

Despite the increasing importance of mobile devices in education, the essential features of these devices for ubiquitous learning have not been empirically addressed. This study empirically investigated the necessary conditions for using mobile devices as an educational tool for ubiquitous learning in higher education by a conjoint method. The results show that respondents want to use Window-based large-screen devices for their educational purposes; thus, current tablet PCs might not be suitable in terms of screen size and type of platform. The findings also implied that potential users want to receive ubiquitous access by using advanced cellular networks, but they do not need comprehensive functions related to office documentation on their mobile devices. Therefore, this study suggests that both policy makers and business players consider developing the optimal educational mobile device as soon as possible for the successful dissemination of ubiquitous learning.
Grid Portal System Based on GPIR

Grid portal is the bridge between Grid and user. In this paper a Grid portal system is set up based on GPIR of GridPort. The Grid portal system provides an efficient means to user for utilizing grid resources, and provides advantaged condition for achieving effective information of database. The user can customize the application by portlet framework. In this paper we also review multiple choices for portal technology and explain why we choose GPIR.
A kinect based control of machine vehicle via body gesture

Kinect sensor is high performance gesture recognition system. Motion of the body is used to communicate with other one is called Gesture. For more accurate gesture recognition sender and receiver have a similar kind of gesture data. In this paper we are focus on gesture command method used to control machine vehicle via body gesture. We develop the kinect based gesture command control method for driving an automated machine vehicle. We integrate the Kinect sensor and process a recording of moving visuals mechanism, the machine capable of carrying out a complex series of action, and control device which incorporates a microprocessor to implement sensible motions control experiments by tracking a human skeleton. For tracking real time moving position of an Operator kinect sensor capture the body movements and moving position is then processed by processing mechanism further sends a command to control vehicle. Proposed system will consist of process to provide a facility to human being to ease their work to drive a vehicle automatically, with the help of kinect sensor camera and processing mechanism to follow the movement of part of body.