gebhart/patrepeval huggingface dataset:
Endogenous silencing of <i><scp>P</scp>uccinia triticina</i> pathogenicity genes through <i>in planta</i>‐expressed sequences leads to the suppression of rust diseases on wheat (2012)

Rust fungi are destructive plant pathogens. The draft genomes of several wheat-infecting species have been released and potential pathogenicity genes identified through comparative analyses to fungal pathogens that are amenable to genetic manipulation. Functional gene analysis tools are needed to understand the infection process of these obligate parasites and to confirm whether predicted pathogenicity genes could become targets for disease control. We have modified an Agrobacterium tumefaciens-mediated in planta-induced transient gene silencing (PITGS) assay for use in Triticum spp. (wheat), and used this assay to target predicted wheat leaf rust fungus, Puccinia triticina (Pt) pathogenicity genes, a MAP kinase (PtMAPK1), a cyclophilin (PtCYC1) and calcineurin B (PtCNB), to analyze their roles in disease. Agroinfiltration effectively delivered hairpin silencing constructs in wheat, leading to the generation of fungal gene-specific siRNA molecules in infiltrated leaves, and resulting in up to 70% reduction in transcription of the endogenous target genes in superinfected Pt. In vivo silencing caused severe disease suppression, compromising fungal growth and sporulation, as viewed by confocal microscopy and measured by reductions in fungal biomass and emergence of uredinia. Interestingly, using the same gene constructs, suppression of infection by Puccinia graminis and Puccinia striiformis was also achieved. Our results show that A. tumefaciens-mediated PITGS can be used as a reverse-genetics tool to discover gene function in rust fungi. This proof-of-concept study indicates that the targeted fungal transcripts might be important in pathogenesis, and could potentially be used as promising targets for developing RNA interference-based resistance against rust fungi.
3-D motion estimation using a sequence of noisy stereo images (2003)

The authors discuss a kinematic-model-based approach for the estimation of 3-D motion parameters from a sequence of noisy stereo images. The approach consists of representing the constant acceleration translational motion and constant angular velocity or constant precession rotational motion in the form of a bilinear state-space model using standard rectilinear states for translation and quaternions for rotation. Closed-form solutions of state transition equations are obtained to propagate the quaternions in both constant-angular-velocity and constant-precession models. The measurements are noisy perturbations of 3-D feature points represented in an inertial coordinate system. It is assumed that the structure is known and that 3-D feature points are extracted from the stereo images and matched over the frames. Owing to the nonlinearity in the state model, nonlinear filters are designed for the estimation of motion parameters.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
FLOTATION AS APPLIED TO MODERN CEMENT MANUFACTURE (1940)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFLOTATION AS APPLIED TO MODERN CEMENT MANUFACTUREG. K. EngelhartCite this: Ind. Eng. Chem. 1940, 32, 5, 645–651Publication Date (Print):May 1, 1940Publication History Published online1 May 2002Published inissue 1 May 1940https://pubs.acs.org/doi/10.1021/ie50365a013https://doi.org/10.1021/ie50365a013research-articleACS PublicationsRequest reuse permissionsArticle Views64Altmetric-Citations-LEARN 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 options Get e-Alerts
Detection of TNT in Water Using an Evanescent Wave Fiber-Optic Biosensor (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDetection of TNT in Water Using an Evanescent Wave Fiber-Optic BiosensorLisa C. Shriver-Lake, Kristen A. Breslin, Paul T. Charles, David W. Conrad, Joel P. Golden, and Frances S. LiglerCite this: Anal. Chem. 1995, 67, 14, 2431–2435Publication Date (Print):July 15, 1995Publication History Published online1 May 2002Published inissue 15 July 1995https://pubs.acs.org/doi/10.1021/ac00110a018https://doi.org/10.1021/ac00110a018research-articleACS PublicationsRequest reuse permissionsArticle Views742Altmetric-Citations112LEARN 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
Low Cost Autonomous Field-Deployable Environment Sensors (2002)

An Autonomous Environmental Sensor (AES) is a miniature electronic package combining position location capability (using the Global Positioning System (GPS)), communications (packet or voice‐synthesized radio), and environmental detection capability (thermal, gas, radiation, optical emissions) into a small, inexpensive, deployable package. AESs can now be made with commercial off‐the‐shelf components. The AES package can be deployed at a study site by airdrop or by workers on the ground, and operates as a data logger (recording data locally) or as a sentry (transmitting data real‐time). Using current low‐power electronics technology, an AES can operate for a number of weeks using a simple dry battery pack, and can be designed to have a transmitting range of several kilometers with current low power radio communication technology. A receiver to capture the data stream from the AES can be made as light, inexpensive and portable as the AES itself. In addition, inexpensive portable repeaters can be used to extend the range of the AES and to coordinate many probes into an autonomous network. We will discuss the design goals and engineering restrictions of an AES, and show a design in a particular application as a wildland fire sentry.
Ehrlichia muris sp. nov., Identified on the Basis of 16S rRNA Base Sequences and Serological, Morphological, and Biological Characteristics (1995)

The 16S rRNA gene of a new infectious agent, strain AS145T (T = type strain), which was isolated from a wild mouse in Japan, was amplified by using the PCR. The amplimers were directly sequenced by dideoxynucleotide methods with Taq DNA polymerase. Sequence comparisons with other members of the tribe Ehrlichieae and related species revealed that the infectious agent isolated from the mouse is a new species of the genus Ehrlichia that is most closely related to Ehrlichia chaffeensis (level of sequence similarity, 97.9%), an agent of human ehrlichiosis in the United States. This result was consistent with the results of an immunoblot analysis performed with immune sera against different ehrlichiosis agents. On the basis of these findings and other morphological, biological, and serological characteristics of the organism, we propose that ehrlichiae with these properties belong to a new species, Ehrlichia muris.
RECOGNITION AND SILENCING OF REPEATED DNA (2000)

Mechanisms for repetition of DNA pose both opportunities and challenges to a functional genome: opportunities for increasing gene expression by amplification of useful sequences, and challenges of controlling amplification by unwanted sequences such as transposons and viruses. Experiments in numerous organisms have suggested the likely existence of a general mechanism for recognition of repeated character in DNA. This review focuses (a) on the nature of these recognition mechanisms, and (b) on types of chromatin modification and gene silencing that are used to control repeated DNA.
Synthesis of ribosomes in Saccharomyces cerevisiae (1989)

The assembly of a eucaryotic ribosome requires the synthesis of four ribosomal ribonucleic acid (RNA) molecules and more than 75 ribosomal proteins. It utilizes all three RNA polymerases; it requires the cooperation of the nucleus and the cytoplasm, the processing of RNA, and the specific interaction of RNA and protein molecules. It is carried out efficiently and is exquisitely sensitive to the needs of the cell. Our current understanding of this process in the genetically tractable yeast Saccharomyces cerevisiae is reviewed. The ribosomal RNA genes are arranged in a tandem array of 100 to 200 copies. This tandem array has led to unique ways of carrying out a number of functions. Replication is asymmetric and does not initiate from every autonomously replicating sequence. Recombination is suppressed. Transcription of the major ribosomal RNA appears to involve coupling between adjacent transcription units, which are separated by the 5S RNA transcription unit. Genes for many ribosomal proteins have been cloned and sequenced. Few are linked; most are duplicated; most have an intron. There is extensive homology between yeast ribosomal proteins and those of other species. Most, but not all, of the ribosomal protein genes have one or two sites that are essential for their transcription and that bind a common transcription factor. This factor binds also to many other places in the genome, including the telomeres. There is coordinated transcription of the ribosomal protein genes under a variety of conditions. However, the cell seems to possess no mechanism for regulating the transcription of individual ribosomal protein genes in response either to a deficiency or an excess of a particular ribosomal protein. A deficiency causes slow growth. Any excess ribosomal protein is degraded very rapidly, with a half-life of 1 to 5 min. Unlike most types of cells, yeast cells appear not to regulate the translation of ribosomal proteins. However, in the case of ribosomal protein L32, the protein itself causes a feedback inhibition of the splicing of the transcript of its own gene. The synthesis of ribosomes involves a massive transfer of material across the nuclear envelope in both directions. Nuclear localization signals have been identified for at least three ribosomal proteins; they are similar but not identical to those identified for the simian virus 40 T antigen. There is no information about how ribosomal subunits are transported from the nucleus to the cytoplasm.(ABSTRACT TRUNCATED AT 400 WORDS)
Temporal raphe of the retinal nerve fiber layer revealed by medullated fibers. (1987)

Three cases of medullated nerve fibers of the retina were seen. They had medullated nerve fibers in both the upper and lower quadrants of the temporal retina, whereby the temporal raphe of the retinal nerve fiber layer could be visualized. Some nerve fibers from the upper and lower quadrants crossed each other on the horizontal meridian. The structure of the temporal raphe reported by Vrabec through anatomical studies was confirmed by ophthalmoscopy.
Contrast in light intensity, rather than day length, influences the behavior and health of broiler chickens (2012)

Day length and intensity are commonly manipulated aspects of the light environment in commercial broiler production. Both influence circadian rhythms, but it is unclear if they do this independently or synergistically. The effect of light:dark (20L:4D, 16L:8D) and intensity contrasts (1 lx:0.5 lx, 200 lx:0.5 lx) on broiler behavior and health (n=1,004, 4 replicates/treatment) was evaluated. Activity was measured using passive infrared detection, and feeding activity was measured by the amount of feed consumed/h over one 24-h period each week. Broilers were gait scored and weighed at 6 wk of age. Following euthanasia, eyes were dissected from 30 birds/treatment. Behavior and performance were analyzed using the GLM, gait score using the Kruskal-Wallis test, and eye measures using a MANOVA. The 200 lx birds were more active (P=0.03) and fed more (P=0.001) during the photophase but were less active (P=0.02) and fed less (P<0.001) during the scotophase, than the 1 lx birds. There were no differences in G:F (mean±SEM, 1.63±0.01 kg of feed/kg of BW). However, 1 lx birds were slightly heavier (2.79±0.01 kg; P=0.02) than 200 lx birds (2.72±0.01 kg). The 200 lx birds had better (P<0.001) mean gait scores than 1 lx birds, although treatment differences were small. One lux birds had greater side-to-side (18.86±0.11 mm vs. 17.63±0.11 mm, P<0.001) and back-to-front (13.39±0.09 mm vs. 12.89±0.09 mm, P<0.001) eye diameters and heavier eyes (2.42±0.03 g vs. 1.99±0.03 g, P<0.001) than 200 lx birds. There was only one effect of light:dark, with 16:8 having greater back-to-front eye diameters than 20:4 (13.30±0.10 mm vs. 13.00±0.10 mm, P=0.02). There were no interactions. These results indicated that light intensity, not day length, was the major factor affecting broiler behavior and health under these lighting conditions. Low contrast light intensity dampened behavioral rhythms and had possible health effects.
trans−cis Photoisomerization of a Photoactive Yellow Protein Model Chromophore in Crystalline Phase (2006)

We have studied the photoinduced trans/cis isomerization of the protonated form of p-hydroxycinnamic thiophenyl ester, a model chromophore of the photoactive yellow protein (PYP), in crystalline phase, by both fluorescence and infrared spectroscopies. The conversion from trans to cis configuration is revealed by a shift of the fluorescence peak and by inspection of the infrared maker bands. The crystal packing apparently stabilizes the cis photoproduct, suggesting different environmental effects from the solvent molecules for this model chromophore in liquid solutions or from the amino acid residues for the PYP chromophore.
Electron Microprobe Analysis and Scanning Electron Microscopy in Geology (2005)

Originally published in 2005, this book covers the closely related techniques of electron microprobe analysis (EMPA) and scanning electron microscopy (SEM) specifically from a geological viewpoint. Topics discussed include: principles of electron-target interactions, electron beam instrumentation, X-ray spectrometry, general principles of SEM image formation, production of X-ray 'maps' showing elemental distributions, procedures for qualitative and quantitative X-ray analysis (both energy-dispersive and wavelength-dispersive), the use of both 'true' electron microprobes and SEMs fitted with X-ray spectrometers, and practical matters such as sample preparation and treatment of results. Throughout, there is an emphasis on geological aspects not mentioned in similar books aimed at a more general readership. The book avoids unnecessary technical detail in order to be easily accessible, and forms a comprehensive text on EMPA and SEM for geological postgraduate and postdoctoral researchers, as well as those working in industrial laboratories.
Design Knowledge and Software Engineering (2001)

This paper points out various relationships between Design Knowledge and Software Engineering. After introduction of human design, the relationships between industrial Software Engineering is discussed, then further details of human design knowledge are revealed with discussions on humanistic aspects of design.
High-throughput evaluation of T7 promoter variants using biased randomization and DNA barcoding (2018)

Cis-regulatory elements (CREs) are one of the important factors in controlling gene expression and elucidation of their roles has been attracting great interest. We have developed an improved method for analyzing a large variety of mutant CRE sequences in a simple and high-throughput manner. In our approach, mutant CREs with unique barcode sequences were obtained by biased randomization in a single PCR amplification. The original T7 promoter sequence was randomized by biased randomization, and the target number of base substitutions was set to be within the range of 0 to 5. The DNA library and subsequent transcribed RNA library were sequenced by next generation sequencers (NGS) to quantify transcriptional activity of each mutant. We succeeded in producing a randomized T7 promoter library with high coverage rate at each target number of base substitutions. In a single NGS analysis, we quantified the transcriptional activity of 7847 T7 promoter variants. We confirmed that the bases from -9 to -7 play an important role in the transcriptional activity of the T7 promoter. This information coincides with the previous researches and demonstrated the validity of our methodology. Furthermore, using an in vitro transcription/translation system, we found that transcriptional activities of these T7 variants were well correlated with the resultant protein abundance. We demonstrate that our method enables simple and high-throughput analysis of the effects of various CRE mutations on transcriptional regulation.
Biaxially oriented poly(ethylene terephthalate) bottles: Effects of resin molecular weight on parison stretching behavior (1981)

Abstract Uni‐ and biaxial stretching of poly(ethylene terephthalate) (PET) specimens of appropriate geometry at temperatures near the glass‐rubber transition may lead to non‐uniform deformation unless the draw ratio exceeds a critical value, the natural draw ratio, characteristic of the onset of strain hardening due to stress‐induced crystallization. Experimental results obtained in the present investigation show that natural draw ratios in uni‐ and biaxial stretching decrease with increasing resin molecular weight and with decreasing temperature. Undesirable uneven wall thickness distribution in biaxially stretched cylindrical parisons can only be prevented if draw ratios in both orthogonal principal stretching directions exceed the corresponding natural values. The minimum thickness reduction required for uniform biaxial stretching of a cylindrical parison at 95°C may vary between 12 and 5 depending on the resin's molecular weight or viscosity and this will affect the optimum design of parison geometry. The degree of unbalanced biaxial molecular orientation in the wall of cylindrical parisons stretched up to or beyond the natural draw ratios also depends on the resin molecular weight. Unbalanced biaxial orientation has been investigated by means of wide angle X‐ray diffraction and birefringence measurements as well as its effect on various properties: rigidity, yield stress, creep compliance, and dimensional stability.
Proximity effect correction in electron-beam lithography (1981)

Electron-beam fabrication offers several important advantages for lithography, including a capability of geometries smaller than one micrometer, a high adaptability to automation and the ability to write directly on a Si wafer without the need for a mask. However, for submicron patterns, a proximity effect is observed by the behavior of incident electrons in a resist. In electron-beam lithography the exposure intensity distribution (hereafter EID) is an essential physical quantity for implementing a proximity effect correction. There are many correction methods and several methods have been tried to correct for practical devices. However, the variation of the EID along the distance into the resist from the surface is neglected, and only a two-dimensional EID is presented in those articles. The present paper describes experimental and theoretical study on a correction method of the proximity effect which contains the consideration of the three-dimensional profile of a resist. It has been found from a Monte Carlo simulation that a cross-sectional profile can be controlled by an additional exposure at the vicinity of a pattern edge. With this method, for example, an undercut resist pattern, which is suitable for a lift-off process, can be obtained, avoiding as a whole the overdose on a pattern. A 0.5 μm line and space pattern with 1 μm thickness PMMA has been easily obtained, namely, when under-developed, the wall profile of the resist becomes rather steep, and when properly developed, the profile becomes undercut.
DNA-Functionalized Quantum Dots: Fabrication, Structural, and Physicochemical Properties (2013)

We have systematically investigated the effect of physicochemical conditions, such as pH, salt concentration, and DNA/nanoparticle ratio, on the chemical conjugation process and structural and optical stability of carboxyl-functionalized quantum dots (QDs) functionalized with amino-modified DNA. We reveal the relationship between aqueous conditions and the amount of DNA conjugated on QDs, colloidal stability, and yield of the final QD-DNA conjugates. By carefully adjusting the environmental variables we have successfully achieved up to 20 DNA strands conjugated per QD, and demonstrated how this number can be tuned. The fabricated QD-DNA conjugates are dispersed and optically stable in salted solutions for over a month. We have also evaluated the involved interparticle interactions to explain the solution behavior of QD-DNA conjugates. Our results provide a basic understanding of the physiochemical processes governing a nanoparticle-biomolecule conjugation and the structural stability of the formed conjugates. Such fabricated QD-DNA conjugates might be of great benefit for programmable assemblies of optically active nanomaterials and for emerging biosensing methods based on nanomaterials.
Scalable interest management using interest group based filtering for large networked virtual environments (2000)

As distributed virtual environment (DVE) scales in terms of users and network latency, a key aspect to consider is scalability for interactive performance because a large number of objects likely impose heavy burden especially on the network and computational resources. To improve the scalability, various relevance-filtering mechanisms and aggregation mechanisms have been proposed. However the existing filtering mechanisms do not scale well in terms of interactive performance as the number of users increases and crowds in a specific place.In this paper, we propose a new scalable filtering scheme that reduces the number of messages by dynamically grouping users based on their interests and distance. Within a group, members communicate with each other with high fidelity. However, a representative sends up-to-dated group information of members with low transmission frequency when they are not of immediate interest but are still within the interest area. The representative is elected from members of the group in distributed manner. The proposed scheme enhances the interactive performance scalability of large-scale DVE systems as much as 18% compared with the existing approach.