gebhart/patrepeval huggingface dataset:
Small RNAs: A New Paradigm in Plant-Microbe Interactions (2014)

A never-ending arms race drives coevolution between pathogens and hosts. In plants, pathogen attacks invoke multiple layers of host immune responses. Many pathogens deliver effector proteins into host cells to suppress host immunity, and many plants have evolved resistance proteins to recognize effectors and trigger robust resistance. Here, we discuss findings on noncoding small RNAs (sRNAs) from plants and pathogens, which regulate host immunity and pathogen virulence. Recent discoveries have unveiled the role of noncoding sRNAs from eukaryotic pathogens and bacteria in pathogenicity in both plant and animal hosts. The discovery of fungal sRNAs that are delivered into host cells to suppress plant immunity added sRNAs to the list of pathogen effectors. Similar to protein effector genes, many of these sRNAs are generated from transposable element (TE) regions, which are likely to contribute to rapidly evolving virulence and host adaptation. We also discuss RNA silencing that occurs between organisms.
GELP: GAN-Excited Linear Prediction for Speech Synthesis from Mel-Spectrogram (2019)

Recent advances in neural network -based text-to-speech have reached human level naturalness in synthetic speech. The present sequence-to-sequence models can directly map text to mel-spectrogram acoustic features, which are convenient for modeling, but present additional challenges for vocoding (i.e., waveform generation from the acoustic features). High-quality synthesis can be achieved with neural vocoders, such as WaveNet, but such autoregressive models suffer from slow sequential inference. Meanwhile, their existing parallel inference counterparts are difficult to train and require increasingly large model sizes. In this paper, we propose an alternative training strategy for a parallel neural vocoder utilizing generative adversarial networks, and integrate a linear predictive synthesis filter into the model. Results show that the proposed model achieves significant improvement in inference speed, while outperforming a WaveNet in copy-synthesis quality.
Swim exercise in <i>Caenorhabditis elegans</i> extends neuromuscular and gut healthspan, enhances learning ability, and protects against neurodegeneration (2019)

Regular physical exercise is the most efficient and accessible intervention known to promote healthy aging in humans. The molecular and cellular mechanisms that mediate system-wide exercise benefits, however, remain poorly understood, especially as applies to tissues that do not participate directly in training activity. The establishment of exercise protocols for short-lived genetic models will be critical for deciphering fundamental mechanisms of transtissue exercise benefits to healthy aging. Here we document optimization of a long-term swim exercise protocol for <i>Caenorhabditis elegans</i> and we demonstrate its benefits to diverse aging tissues, even if exercise occurs only during a restricted phase of adulthood. We found that multiple daily swim sessions are essential for exercise adaptation, leading to body wall muscle improvements in structural gene expression, locomotory performance, and mitochondrial morphology. Swim exercise training enhances whole-animal health parameters, such as mitochondrial respiration and midlife survival, increases functional healthspan of the pharynx and intestine, and enhances nervous system health by increasing learning ability and protecting against neurodegeneration in models of tauopathy, Alzheimer's disease, and Huntington's disease. Remarkably, swim training only during early adulthood induces long-lasting systemic benefits that in several cases are still detectable well into midlife. Our data reveal the broad impact of swim exercise in promoting extended healthspan of multiple <i>C. elegans</i> tissues, underscore the potency of early exercise experience to influence long-term health, and establish the foundation for exploiting the powerful advantages of this genetic model for the dissection of the exercise-dependent molecular circuitry that confers system-wide health benefits to aging adults.
ESD protection design for differential low-noise amplifier with cross-coupled SCR (2010)

A new electrostatic discharge (ESD) protection scheme for differential low-noise amplifier (LNA) was proposed in this paper. The new ESD protection scheme, which evolved from the conventional double-diode ESD protection scheme without adding any extra device, was realized with cross-coupled silicon-controlled rectifier (SCR). With the new ESD protection scheme, the pin-to-pin ESD robustness can be improved, which was the most critical ESD-test pin combination for differential input pads. Experimental results had shown that differential LNA with cross-coupled-SCR ESD protection scheme can achieve excellent ESD robustness and good RF performances.
Introduction of Cloning Plasmids into Agrobacterium tumefaciens (2003)

Most experiments utilizing Agrobacterium tumefaciens as a vector for the introduction of genes into plant cells commence in Escherichia coli. The sheer size and complexity of the Ti-plasmids precludes their direct manipulation. Thus, insertion is usually into a comparatively small binary vector, which is then propagated in E. coli, before being introduced into A. tumefaciens, where the larger, complementing vir plasmid mediates gene transfer to plants. Typically, the binary plasmid will be based on a broad host range replicon, of IncP, IncQ, or IncW derivation, capable of replication in both bacterial hosts. Its construction will have resulted in the binary plasmid possessing the following features:
A mathematical model of Clostridium difficile transmission in medical wards and a cost-effectiveness analysis comparing different strategies for laboratory diagnosis and patient isolation (2017)

CDI can be decreased by better isolation and more sensitive laboratory methods. From the hospital perspective, improving isolation is more cost-effective than improving diagnostics.
Endophytes of annual and hybrid ryegrasses (1988)

Abstract Endophytes of Lotium spp. were studied, with particular emphasis on those in annual and hybrid ryegrasses. A previously undescribed Acremonium ‐like species of endophyte has been isolated from Lotium multijiorum, Lotium × hybridum cv. Grasslands Manawa, and six species and varieties of annual Lotium spp. This fungus has been cultured and successfully inoculated into seedlings of L. multijiorum . Mycelium occurs in nodes, leaf sheath bases, culms, and seeds of infected plants. It is common in most New Zealand cultivars and ecotypes of L. multijiorum but not in cultivars from overseas. Mycelium of a second endophyte, a Gliocladiumlike sp., occurred in plants of L. multijiorum, L . × hybridum , and L. perenne , but mycelium of a third endophyte, A. lolii , was found only in L. perenne and L . × hybridum cv. Grasslands Ariki. Seedlings of L. multijiorum, L. temulentum , and ‘Grasslands Manawa’ were artificially infected with A. lolii . Mycelium of this fungus was not confined to the base of leaf sheaths of these plants but grew throughout the sheath.
Physicochemical Characterization of AlCl<sub>3</sub>–1-Ethyl-3-methylimidazolium Chloride Ionic Liquid Electrolytes for Aluminum Rechargeable Batteries (2017)

Al-ion batteries technology is receiving growing attention thanks to the high natural abundance of aluminum and to the high energy density that can be obtained with a three-electron redox process. In this work, the physicochemical properties of the room temperature ionic liquid composed of aluminum chloride and 1-ethyl-3-methylimidazolium chloride ([EMIm]Cl) were systematically investigated by varying the molar ratio AlCl3/[EMIm]Cl in the range 1.1–1.7. The combined use of multinuclear (27Al, 13C, 1H) NMR, electrochemical impedance spectroscopy, and thermal analysis allowed us to shed light on the structure–properties relationships of this complex system, also resolving some controversial conclusions of previous literature. We showed that the 1.2 molar ratio is the best compromise between high ionic conductivity and the use of the highly toxic AlCl3. This electrolyte was tested in a standard Al-ion cell and gave promising results even at very high current densities (i > 200 mA g–1).
A Frequency-Modulation Station Monitor (1942)

This paper describes the development, theory, and characteristics of a frequency-modulation station monitor developed in the general engineering laboratory of the General Electric Company. The monitor measures mean carrier frequency with and without modulation and the percentage of frequency modulation as a percentage of 75-kilocycle deviation. In addition, it provides a flasher and alarm circuit for overmodulation adjustable from 50 to 120 per cent and an audio-frequency fidelity monitoring circuit. The paper begins with a discussion of the requirements for frequency-modulation monitors and compares the problems involved with those involved in standard broadcast monitors. Several schemes which were examined for use as a frequency-modulation monitor are briefly described, including counter and frequency-division systems. The principles and design of the final monitor are discussed. The last part of the paper is devoted to a discussion of the salient development problems encountered, to a detailed description of the circuit, and to a discussion of the over-all specifications of the commercial sample.
Microarray pattern recognition based on PtII terpyridyl chloride complexes: vapochromic and vapoluminescent response (2008)

Eighteen distinct Pt(II) terpyridyl chloride cross-reactive sensor elements incorporated into microarrays with 1000 x 250 microm well dimensions generate distinctive colorimetric and luminometric responses upon exposure to a variety of volatile organic compounds (VOCs).
Fabrication of photonic quantum ring laser using chemically assisted ion beam etching (2001)

This article presents an etching process to fabricate a high-quality vertical facet for the photonic quantum ring (PQR) laser. The presented process uses the chemically assisted ion beam etching (CAIBE) method with a gas mixture of Ar:Cl2:BCl3=5:2:3 sccm, and uses a single-layer photoresist etch mask to reduce the process complexity of etching GaAs/AlGaAs structures for the PQR laser. The angle θ between the incident beam and the normal direction of the substrate has been adjusted to achieve a high-quality vertical facet. Distortions on the mask pattern are not transferred to the etched side wall for θ⩾25°, and a vertical facet is obtained at θ∼25°. The fabricated PQR lasers with the CAIBE process in this article show a sharp linewidth of ∼0.06 nm.
<i>In Utero</i> Gene Therapy: Transfer and Long-Term Expression of the Bacterial <i>neo</i> <sup>r</sup> Gene in Sheep after Direct Injection of Retroviral Vectors into Preimmune Fetuses (1998)

We investigated whether directly injecting retroviral vectors into preimmune fetuses could result in the transfer and long-term expression of exogenous genes. Twenty-nine preimmune sheep fetuses were injected with helper-free retroviral vector preparations. Twenty-two fetuses survived to term, 4 of which were sacrificed at birth. Of the remaining 18 animals, 3 were controls and 15 had received vector preparations. Twelve of these 15 animals demonstrated transduction of hematopoietic cells when blood and marrow were analyzed by neo(r)-specific PCR. Eight experimental sheep have been followed for 5 years, during which time we have consistently observed proviral DNA and G418-resistant hematopoetic progenitors. The G418-resistant colonies were positive when analyzed by neo(r)-specific PCR. neo(r) gene expression was also demonstrated using several immunological and biochemical methods. The transduction of hematopoietic stem cells was confirmed when lambs transplanted with bone marrow from in utero-transduced sheep exhibited neo(r) activity in marrow and blood. Vector distribution was widespread in primary animals without pathology. PCR analysis indicates that the germ line was not altered. These studies demonstrate that direct injection of an engineered retrovirus is a feasible means of safely delivering a foreign gene to a developing fetus and achieving long-term expression without modifying the germ line of the recipient.
Pregnancy hormones, estrogen and progesterone, prevent HIV‐1 synthesis in monocytes but not in lymphocytes (1992)

Increase in levels of estrogen and progesterone during pregnancy may affect intra-uterine HIV-1 infection through their effect on maternal immunocompetent cells. These hormones were examined for containing HIV-1 production from ACH-2 lymphocytes and U1 monocytes. Neither of the hormones has an effect on ACH-2, but with U1, the physiological concentrations (0.1 microgram 0.1 ng) of progesterone and estrogen demonstrate significant inhibition of HIV-1 release. Except for the highest dose of 1 microgram/ml, the dose-response to progesterone and estrogen was not correlated with the negative influence on proliferation of both types of cells. The results suggest that in vivo low doses of female steroids may display specific antiviral activity in monocytes but not in lymphocytes.
Learning object recognition models from images (2002)

To recognize an object in an image an internal model is required to indicate how that object may appear. The authors show how to learn such a model from a series of training images depicting a class of objects, producing a model that represents a probability distribution over the variation in object appearance. Features identified in an image through perceptual organization are represented by a graph whose nodes include feature labels and numeric measurements. A learning procedure generalizes multiple image graphs to form a model graph in which the numeric measurements are characterized by probability distributions. A matching procedure, using a similarity metric based on a non-parametric probability density estimator, compares model and image graphs to identify an instance of a modeled object in an image. Experimental results are presented from a system constructed to test this approach. The system learns to recognize partially occluded 2-D objects in 2-D images using shape cues. It can recognize objects as similar in general appearance while distinguishing them by their detailed features. >
Spreading of Multi-component Oils on Water (2012)

The spreading of multi-component oils on water has been investigated by direct observations and predicted from measurements of the interfacial tensions and surface tensions of decane, toluene, heptane, and their mixtures. Pure decane does not naturally spread at ambient conditions, as indicated by its negative spreading coefficient. However, when decane is mixed with toluene and heptane, the mixture spreads on water over a wide range of compositions. The spreading coefficients are highly nonlinear with respect to concentration and feature a maximum. The spreading is ascribed to preferential accumulation of toluene at the oil/water interface and heptane at the oil/vapor interface. Molecular dynamics simulations corroborate the hypothesis of preferential accumulation. The accumulation of lighter alkanes at the oil/vapor interface reduces the surface tension, and the accumulation of aromatics at the oil/water interface decreases the interfacial tension. As a consequence, the oil mixture spreads over water.
Comparison of Design Strategies for Promotion of β‐Peptide 14‐Helix Stability in Water (2008)

Many short beta-peptides adopt well-defined conformations in organic solvents, but specialized stabilizing elements are required for folding to occur in aqueous solution. Several different strategies to stabilize the 14-helical secondary structure in water have been developed, and here we provide a direct comparison of three such strategies. We have synthesized and characterized beta-peptide heptamers in which variously a salt bridge between side chains, a covalent link between side chains, or two cyclically constrained residues have been incorporated to promote 14-helicity. The incorporation of a salt bridge does not generate significant 14-helicity in water, according to CD and 2D NMR data. In contrast, incorporation either of a lactam bridge between side chains or of cyclic residues results in stable 14-helices in water. The beta-peptides featuring trans-2-aminocyclohexanecarboxylic acid (ACHC) residues show the highest 14-helical backbone stability, with hardly any sensitivity to pH or ionic strength. The beta-peptides featuring side-chain-to-side-chain cyclization show lower 14-helical backbone stability and higher sensitivity to pH and ionic strength, but increased order between the side chains because of the cyclization.
Geometric morphometric approaches to the study of sexual size dimorphism in mammals (2000)

<strong>Abstract</strong> Sexual size dimorphism (SSD) has been extensively documented in many organisms, from vascular plants to vertebrates, including mammals. Geometric morphometric methods offer new, powerful tools for the study of SSD. The investigation of shape variability has not been previously pursued in traditional SSD studies and is an unique contribution of geometric morphometrics to this field. The combining of Procrustes methods with multivariate statistical analyses supports all traditional SSD experimental designs and allows new studies of shape variability and its relationship with size and other variables. Intraspecific and interspecific examples comparing traditional and geometric morphometric approaches to the study of SSD within several mammalian taxa are presented.
High spatial resolution semi‐automatic crystallite orientation and phase mapping of nanocrystals in transmission electron microscopes (2011)

Abstract A semi‐automatic technique for the mapping of nanocrystal phases and orientations in a transmission electron microscope (TEM) is described. It is based primarily on the projected reciprocal lattice geometry, but also utilizes the intensity of reflections that are extracted from precession‐enhanced electron diffraction spot patterns of polycrystalline materials and multi‐material composites. At the core of the method, experimental (precession‐enhanced) electron diffraction spot patterns are cross correlated with pre‐calculated templates for a set of model structures. The required hardware facilitates a scanning‐precession movement of the primary electron beam on the polycrystalline and/or multi‐material sample and can be interfaced to any newer or older mid‐voltage TEM. The software that goes with this hardware is so flexible in its intake of experimental data that it can also create crystallite orientation and phase maps of nanocrystals from the amplitude part of Fourier transforms of high resolution TEM images. Experimentally obtained crystallite orientation and phase maps are shown for a clausthalite nanocrystal powder sample, polycrystalline aluminum and copper films, fine‐grained palladium films, as well as MnAs crystallites that are partly embedded in a GaAs wafer. Comprehensive open‐access and commercial crystallographic databases that may provide reference data in support of the nanocrystal phase identification process of the software are briefly mentioned. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Water Eliminated Fourier Transform NMR Spectroscopy (1972)

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Penile Prosthetic Surgery under Local Anesthesia (1982)

Local anesthesia is effective for implantation of the semirigid rod and the inflatable penile prostheses. Pudendal block, and intracorporeal and local infiltration provide excellent opportunities to perform this operation with rare need for general anesthesia supplementation. The technique is described in 141 cases.
Increased expression of nitric oxide synthase in the myometrium of the pregnant rat uterus (1997)

Nitric oxide (NO) relaxes uterine smooth muscle and is produced by the pregnant uterus. Our previous studies revealed an increase in rat uterine NO synthase (NOS) activity in pregnancy and a decline at term. In the present study, we have examined the distribution of NOS isoform expression to determine whether their regulation is consistent with a role in the inhibition of uterine contractions before term. At day 17-18 of pregnancy, NOS immunohistochemistry revealed expression of two isoforms: endothelial constitutive form of NOS (ecNOS) in vascular endothelium and inducible form of NOS (iNOS) in myometrial and vascular smooth muscle and in decidual epithelium. Immunoblotting revealed that expression of iNOS declined nearly fivefold, whereas ecNOS declined twofold in laboring rats at term. We conclude that iNOS is expressed in myometrium of pregnant rat uterus but not the virgin rat and that iNOS expression declines at term when labor is present. The pattern of changes in myometrial iNOS expression with advancing gestation suggests that NO could act in an autocrine and/or paracrine manner to inhibit uterine contractions before term.
Non-negative matrix factorization by maximizing correntropy for cancer clustering (2013)

Abstract Background Non-negative matrix factorization (NMF) has been shown to be a powerful tool for clustering gene expression data, which are widely used to classify cancers. NMF aims to find two non-negative matrices whose product closely approximates the original matrix. Traditional NMF methods minimize either the l 2 norm or the Kullback-Leibler distance between the product of the two matrices and the original matrix. Correntropy was recently shown to be an effective similarity measurement due to its stability to outliers or noise. Results We propose a maximum correntropy criterion (MCC)-based NMF method (NMF-MCC) for gene expression data-based cancer clustering. Instead of minimizing the l 2 norm or the Kullback-Leibler distance, NMF-MCC maximizes the correntropy between the product of the two matrices and the original matrix. The optimization problem can be solved by an expectation conditional maximization algorithm. Conclusions Extensive experiments on six cancer benchmark sets demonstrate that the proposed method is significantly more accurate than the state-of-the-art methods in cancer clustering.
Transition metal‐catalyzed tandem isomerization and cationic polymerization of allyl ethers. I. Discovery and scope (1997)

Allyl ethers are readily polymerized using a new polymerization reaction termed: transition metal-catalyzed tandem isomerization and cationic polymerization. Employing dicobalt octacarbonyl in combination with organosilanes, polymerization takes place rapidly and exothermically to give high molecular weight polymers. In this first article, the concepts leading to the discovery of this novel type of polymerization are presented along with the results of initial studies. © 1997 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 35: 1593–1604, 1997
Increase of Plasma IL-12/p40 Ratio Induced by the Combined Therapy of DNA Vaccine and Lamivudine Correlates with Sustained Viremia Control in CHB Carriers (2009)

Our results indicate that the combined therapy induces the increase of plasma IL-12 and IL-12/p40 ratio, which are associated with long-term SVR in CHB carriers.
A Selective Estrogen Receptor Modulator for the Treatment of Hot Flushes (2006)

A selective estrogen receptor modulator (SERM) for the potential treatment of hot flushes is described. (R)-(+)-7,9-difluoro-5-[4-(2-piperidin-1-ylethoxy)phenyl]-5H-6-oxachrysen-2-ol, LSN2120310, potently binds ERalpha and ERbeta and is an antagonist in MCF-7 breast adenocarcinoma and Ishikawa uterine cancer cell lines. The compound is a potent estrogen antagonist in the rat uterus. In ovariectomized rats, the compound lowers cholesterol, maintains bone mineral density, and is efficacious in a morphine dependent rat model of hot flush efficacy.