gebhart/patrepeval huggingface dataset:
Three of four pseudoknots in tmRNA are interchangeable and are substitutable with single‐stranded RNAs (2000)

A novel translation, trans-translation, is facilitated by a highly structured RNA molecule, tmRNA. This molecule has two structural domains, a tRNA domain and an mRNA domain, the latter including four pseudoknot structures (PK1 to PK4). Here, we show that replacement of each of these pseudoknots, except PK1, in Escherichia coli tmRNA with a single stranded RNA did not seriously affect the functions as an alanine tRNA and as an mRNA. Furthermore, these three pseudoknots were interchangeable with only small losses of the two functions. These findings suggest that neither PK2, PK3 nor PK4 interacts in a functional manner with ribosome during the trans-translation process. Together with an earlier study showing the significance of PK1, it is concluded that among the four pseudoknots, PK1 is the most functional.
(Electrochemical hydrogenation and hydrogenolysis in aqueous media) (1989)

We focused on preparative reductions at mercury cathodes in media containing tetraalkylammonium (TAA{sup +}) electrolytes. Using these conditions the cathodic reduction of functional groups which are electroinactive within the accessible potential window'' has been achieved and several simple, but selective organic syntheses were performed. Quite a number of functional groups are reduced at this limit of the cathodic potential window.'' The reduction of benzene, alkynes, alkenes, polycyclic aromatic hydrocarbons, phenanthrene, and benzothiophene is described. The research could be applied to areas such as coal hydrogenation. 6 tabs.
Hyperspectral Microscope Imaging Methods to Classify Gram-Positive and Gram-Negative Foodborne Pathogenic Bacteria (2015)

<abstract><title><italic>Abstract.</italic></title> An acousto-optic tunable filter (AOTF)-based hyperspectral microscope imaging (HMI) method has potential for rapid identification of foodborne pathogenic bacteria from micro-colonies with a cell level. In this study, we successfully developed a method to acquire quality hyperspectral microscopic images from various gram-negative and gram-positive bacteria live cells. Among the contiguous spectral images from the visible/NIR region between 450 and 800 nm, the scattering intensity of spectral images was distinct at mostly visible wavelengths. Specifically, the scattering peak intensity was distinct at 458, 498, 522, 546, 574, 590, 646, 670, and 690 nm for Staphylococcus. Similarly, distinct peak spectra were observed at 462, 498, 522, 546, 574, 598, 642, 670, and 690 nm for Salmonella. For both cases, the scattering intensity of outer cell membranes was brighter than that of inner membranes except at 546 nm, which was possibly caused by excitation of the metal-halide lighting source. The scattering intensity from a single cell varied with the wavelength as well as the type of bacteria. The overall variability of intensity was 31.2% for gram-negative (Salmonella) and 42.7% for gram-positive (Staphylococcus) bacteria. With scattering intensity data from five serotypes of Salmonella (Kentucky, Enteritidis, Typhimurium, Infantis, and Heidelberg) and five species of Staphylococcus (aureus, haemolyticus, hyicus, simulans, and sciuri) bacterial cells, a classification accuracy of 99.9% with a kappa coefficient of 0.9998 was obtained from the support vector machine (SVM) classification algorithm.
Cognitive deficits in progressive supranuclear palsy, Parkinson's disease, and multiple system atrophy in tests sensitive to frontal lobe dysfunction. (1994)

Groups of patients with idiopathic Parkinson's disease, multiple system atrophy, and progressive supranuclear palsy or Steele-Richardson-Olszewski syndrome, matched for overall clinical disability, were compared using three computerised cognitive tests previously shown to be sensitive to frontal lobe dysfunction. On a test of planning based on the Tower of London task, all three groups were impaired, but in different ways. The groups with palsy and Parkinson's disease were slower in the measure of initial thinking time, whereas the group with multiple system atrophy was only slower in a measure of thinking time subsequent to the first move, resembling patients with frontal lobe damage. On a test of spatial working memory, each group showed deficits relative to their matched control groups, but the three groups differed in their strategy for dealing with this task. On a test of attentional set shifting, each group was again impaired, mainly at the extradimensional shifting stage, but the group with Steele-Richardson-Olszewski syndrome exhibited the greatest deficit. The results are compared with previous findings in patients with Alzheimer's disease or frontal lobe damage. It is concluded that these basal ganglia disorders share a distinctive pattern of cognitive deficits on tests of frontal lobe dysfunction, but there are differences in the exact nature of the impairments, in comparison not only with frontal lobe damage but also with one another.
Comparative Evaluation of Collocation Extraction Metrics. (2002)

Corpus-based automatic extraction of collocations is typically carded out employing some statistic indicating concurrency in order to identify words that co-occur more often than expected by chance. In this paper we are concerned with some typical measures such as the t-score, Pearson&apos;s z-square test, log-likelihood ratio, pointwise mutual information and a novel information theoretic measure, namely mutual dependency. Apart from some theoretical discussion about their correlation, we perform comparative evaluation experiments judging performance by their ability to identify lexically associated bigrams. We use two different gold standards: WordNet and lists of named-entities. Besides discovering that a frequency-biased version of mutual dependency performs the best, followed close by likelihood ratio, we point out some implications that usage of available electronic dictionaries such as the WordNet for evaluation of collocation extraction encompasses.
Evaluación de tres sustratos sobre el desempeño productivo y reproductivo de lombriz roja californiana (Eisenia foetida) (2021)

El presente trabajo realizo un precomposteo de la ovinaza, bovinaza y desechos de cocina. Se realizo analisis de pH, humedad y temperatura, al finalizar el experimento se determino la biomasa. Se aislaron las lombrices de los sustratos y se cuantificaron como indicador de factibilidad de sustratos. Los resultados fueron analizados bajo un diseno completamente al azar, realizando una prueba de tukey para comparar los promedios. Del dia 1 a 8 el pH de la ovinaza fue mas alto y se mantuvo alcalino durante todo el ciclo experimental contrastando con los sustratos de bovinaza y desechos de cocina (p 0.05), en los dos tratamientos hubo un buen rendimiento en la produccion, se presento gran cantidad de lombrices juveniles que representan la reproduccion de esta lombriz, y el buen funcionamiento del sustrato.
Contribution of Nitric Oxide Synthases 1, 2, and 3 to Airway Hyperresponsiveness and Inflammation in a Murine Model of Asthma (1999)

Asthma is a chronic disease characterized by increased airway responsiveness and airway inflammation. The functional role of nitric oxide (NO) and the various nitric oxide synthase (NOS) isoforms in human asthma is controversial. To investigate the role of NO in an established model of allergic asthma, mice with targeted deletions of the three known isoforms of NOS (NOS1, 2, and 3) were studied. Although the inducible (NOS2) isoform was significantly upregulated in the lungs of ovalbumin (OVA)-sensitized and -challenged (OVA/OVA) wild-type (WT) mice and was undetectable in similarly treated NOS2-deficient mice, airway responsiveness was not significantly different between these groups. OVA/OVA endothelial (NOS3)-deficient mice were significantly more responsive to methacholine challenge compared with similarly treated NOS1 and NOS1&3-deficient mice. Airway responsiveness in OVA/OVA neuronal (NOS1)-deficient and neuronal/endothelial (NOS1&3) double-deficient mice was significantly less than that observed in similarly treated NOS2 and WT groups. These findings demonstrate an important function for the nNOS isoform in controlling the inducibility of airway hyperresponsiveness in this model of allergic asthma.
Cidofovir and Experimental Herpetic Stromal Disease (1999)

Cidofovir is a new, potent antiviral that seems similar in efficacy to trifluridine and is effective in the prevention of the development of stromal herpes, but is not effective in the treatment of established stromal disease in which hypersensitivity predominates.
Interpolation over Light Fields with Applications in Computer Graphics (2003)

We present a data structure, called a ray interpolant tree, orRI-tree, which stores a discrete set of directed lines in 3-space, each represented as a point in 4-space. Each directed line is associated with some small number of continuous geometric attributes. We show how this data structure can be used for answering interpolation queries, in which we are given an arbitrary ray in 3-space and wish to interpolate the attributes of neighboring rays in the data structure. We illustrate the practical value of the RI-tree in two applications from computer graphics: ray tracing and volume visualization. In particular, given objects defined by smooth curved surfaces, the RI-tree can produce high-quality renderings significantly faster than standard methods. We also investigate a number of tradeoffs between the space and time used by the data structure and the accuracy of the interpolation results.
Integration of an unmanned vehicle and its application to real-time gas detection and monitoring (2015)

A real-time aerial gas detection and monitoring system is developed for air quality control in China Steel Corporation (CSC). A gas detection module is integrated with an quadrotor and the collected gas information is going to be delivered to a ground station through wireless communication. According to the measurement data, real-time and post analyses will be applied and the results could also be passed to product line for references and other applications. Moreover, image process technology is also integrated into the flight system such that a selected target could be detected automatically during the flight task. Finally, experiments are presented to demonstrate the main concept of the prototype system.
Protein Signature of Lung Cancer Tissues (2012)

Lung cancer remains the most common cause of cancer-related mortality. We applied a highly multiplexed proteomic technology (SOMAscan) to compare protein expression signatures of non small-cell lung cancer (NSCLC) tissues with healthy adjacent and distant tissues from surgical resections. In this first report of SOMAscan applied to tissues, we highlight 36 proteins that exhibit the largest expression differences between matched tumor and non-tumor tissues. The concentrations of twenty proteins increased and sixteen decreased in tumor tissue, thirteen of which are novel for NSCLC. NSCLC tissue biomarkers identified here overlap with a core set identified in a large serum-based NSCLC study with SOMAscan. We show that large-scale comparative analysis of protein expression can be used to develop novel histochemical probes. As expected, relative differences in protein expression are greater in tissues than in serum. The combined results from tissue and serum present the most extensive view to date of the complex changes in NSCLC protein expression and provide important implications for diagnosis and treatment.
The use of guard bands to mitigate multiple access interference in the OFDMA uplink (2008)

Abstract — The usual approach to mitigate multiple access interference (MAI) in the uplink of cellular OFDMA based systems is to use relatively large cyclic prefixes as time domain guard periods. In this paper, we suggest to use a combination of short time domain guard periods and frequency domain guard bands to protect against MAI instead. Guard bands can be added and removed as necessary and, thus, increase the MAI protection flexibility. We show that, if optimally applied, the use of guard bands can significantly increase the system’s uplink capacity or minimum capacity per user. 1 I.
Intraperitoneal chemotherapy for ovarian cancer (2006)

Based on recent findings, intraperitoneal chemotherapy should be considered for the front-line treatment of women with minimal residual advanced ovarian cancer. Efforts should continue to facilitate the integration of intraperitoneal treatment into mainstream practice, and future trials should be designed to address lingering controversy surrounding this route of treatment.
Polymer Melt Fracture (2010)

The continually growing plastics market consists of more than 250 million tons of product annually, making the recurring problem of polymer melt fracture an acute issue in the extrusion of these materials. Presenting a pictorial library of the different forms of melt fracture and real industrial extrusion melt fracture phenomena, Polymer Melt Fract
The Polygalacturonase-Inhibiting Protein PGIP2 of <i>Phaseolus vulgaris</i> Has Evolved a Mixed Mode of Inhibition of Endopolygalacturonase PG1 of <i>Botrytis cinerea</i> (2005)

Botrytis cinerea is a phytopathogenic fungus that causes gray mold in >1,000 plant species. During infection, it secretes several endopolygalacturonases (PGs) to degrade cell wall pectin, and among them, BcPG1 is constitutively expressed and is an important virulence factor. To counteract the action of PGs, plants express polygalacturonase-inhibiting proteins (PGIPs) that have been shown to inhibit a variety of PGs with different inhibition kinetics, both competitive and noncompetitive. The PG-PGIP interaction promotes the accumulation of oligogalacturonides, fragments of the plant cell wall that are general elicitors of plant defense responses. Here, we characterize the enzymatic activity of BcPG1 and investigate its interaction with PGIP isoform 2 from Phaseolus vulgaris (PvPGIP2) by means of inhibition assays, homology modeling, and molecular docking simulations. Our results indicate a mixed mode of inhibition. This is compatible with a model for the interaction where PvPGIP2 binds the N-terminal portion of BcPG1, partially covering its active site and decreasing the enzyme affinity for the substrate. The structural framework provided by the docking model is confirmed by site-directed mutagenesis of the residues that distinguish PvPGIP2 from the isoform PvPGIP1. The finding that PvPGIP2 inhibits BcPG1 with a mixed-type kinetics further indicates the versatility of PGIPs to evolve different recognition specificities.
Sodium and potassium vapor Faraday filters revisited: theory and applications (2009)

A complete theory describing the transmission of atomic vapor Faraday filters is developed. The dependence of the filter transmission on atomic density and external magnetic field strength, as well as the frequency dependence of transmission, are explained in physical terms. As examples, applications of the computed results to ongoing research to suppress sky background, thus allowing Na lidar operation under sunlit conditions, and to enable measurement of the density of mesospheric oxygen atoms are briefly discussed.
Persistent pruritus after hydroxyethyl starch infusion therapy: a result of long-term storage in cutaneous nerves. (1997)

A high incidence of severe pruritus has been observed after the administration of hydroxyethyl starch (HES) on account of plasma volume substitution and improvement of the microcirculation. The aim of this study was to elucidate the possible pathomechanisms of HES-induced itching. Skin biopsies were taken from 93 patients, half of them presenting with pruritus, who received HES of various preparations and cumulative dosages. The samples were subjected to immunoelectron microscopical investigation using an antibody highly specific for HES. After infusion therapy with HES, formation of intracytoplasmic storage vacuoles in the skin could be demonstrated in all patients. A dose-dependent uptake of HES was first detectable in macrophages and, thereafter, in endothelial and epithelial cells. Consecutive control biopsies taken from single patients revealed a subsequent reduction of the vacuoles, in size and number, within 3 years, thus indicating a regular cutaneous metabolism of HES. Patients suffering from pruritus consistently showed additional deposition of HES in small peripheral nerves. HES-reactive vacuoles could be demonstrated in the Schwann cells of unmyelinated, as well as small myelinated, nerve fibres, and in endoneural and perineural cells. Neural devacuolization paralleled the clinical improvement in the symptoms. In conclusion, HES deposits in cutaneous nerves, as a consequence of a higher cumulative dosage, may account for the itching seen after HES infusion.
Immunotherapy of murine sarcoma by adoptive transfer of resident peritoneal macrophages proliferating in culture. (1988)

Normal resident peritoneal macrophages from BALB/c mice were continuously grown and expanded in vitro as non tumorigenic cells on a confluent layer of mesothelial cells. These peritoneal macrophages expanded in vitro (EPM) were very cytotoxic against EMT6 sarcoma, Abelson myeloma, EL4, and L929S cells in culture. This tumoricidal effect was fully expressed without further activation with bacterial lipopolysaccharides (LPS). In vivo, adoptive transfer of one million EPM to BALB/c mice bearing subcutaneous EMT6 sarcoma caused regression of the solid tumor. In contrast, macrophages produced by 10 days' culture of bone marrow stem cells, or freshly isolated from the peritoneal cavity of BALB/c mice, were not cytotoxic in vitro or in vivo. Local injection in the vicinity of the tumor as well as intravenous transplantation of EPM effectively inhibited tumor growth. This antitumoral effect was further enhanced by intraperitoneal injection of 2 micrograms LPS to the tumor bearing mice.
Marital Dissolution and Family Solidarity (1981)

Presented at the AMCAP convention October 3, 1980.
Lipedema: A Relatively Common Disease with Extremely Common Misconceptions (2016)

Lipedema, or adiposis dolorosa, is a common adipose tissue disorder that is believed to affect nearly 11% of adult women worldwide. It is characterized most commonly by disproportionate adipocyte hypertrophy of the lower extremities, significant tenderness to palpation, and a failure to respond to extreme weight loss modalities. Women with lipedema report a rapid growth of the lipedema subcutaneous adipose tissue in the setting of stress, surgery, and/or hormonal changes. Women with later stages of lipedema have a classic "column leg" appearance, with masses of nodular fat, easy bruising, and pain. Despite this relatively common disease, there are few physicians who are aware of it. As a result, patients are often misdiagnosed with lifestyle-induced obesity, and/or lymphedema, and subjected to unnecessary medical interventions and fat-shaming. Diagnosis is largely clinical and based on criteria initially established in 1951. Treatment of lipedema is effective and includes lymphatic support, such as complete decongestive therapy, and specialized suction lipectomy to spare injury to lymphatic channels and remove the diseased lipedema fat. With an incidence that may affect nearly 1 in 9 adult women, it is important to generate appropriate awareness, conduct additional research, and identify better diagnostic and treatment modalities for lipedema so these women can obtain the care that they need and deserve.
Degradation of Morpholine by an Environmental <i>Mycobacterium</i> Strain Involves a Cytochrome P-450 (1998)

A Mycobacterium strain (RP1) was isolated from a contaminated activated sludge collected in a wastewater treatment unit of a chemical plant. It was capable of utilizing morpholine and other heterocyclic compounds, such as pyrrolidine and piperidine, as the sole source of carbon, nitrogen, and energy. The use of in situ 1H nuclear magnetic resonance (1H NMR) spectroscopy allowed the determination of two intermediates in the biodegradative pathway, 2-(2-aminoethoxy)acetate and glycolate. The inhibitory effects of metyrapone on the degradative abilities of strain RP1 indicated the involvement of a cytochrome P-450 in the biodegradation of morpholine. This observation was confirmed by spectrophotometric analysis and 1H NMR. Reduced cell extracts from morpholine-grown cultures, but not succinate-grown cultures, gave rise to a carbon monoxide difference spectrum with a peak near 450 nm, which indicated the presence of a soluble cytochrome P-450. 1H NMR allowed the direct analysis of the incubation medium containing metyrapone, a specific inhibitor of cytochrome P-450. The inhibition of morpholine degradation was dependent on the morpholine/metyrapone ratio. The heme-containing monooxygenase was also detected in pyrrolidine- and piperidine-grown cultures. The abilities of different compounds to support strain growth or the induction of a soluble cytochrome P-450 were assayed. The results suggest that this enzyme catalyzes the cleavage of the C-N bond of the morpholine ring.
Optical coherence tomography enables imaging of tumor initiation in the TAg-RB mouse model of retinoblastoma. (2015)

OCT is a non-invasive imaging modality for tracking early TAg-RB tumor growth in vivo. Using OCT, we characterized TAg-positive cells as early as 2 weeks, corresponding to the earliest stages at which tumors are histologically evident, and well before they are evident with funduscopy. Tracking tumor growth from its earliest stages will allow better analysis of the efficacy of novel therapeutics and genetic factors tested in this powerful mouse model.
A procedure to determine the optimum imaging parameters for atomic/molecular resolution frequency modulation atomic force microscopy (2010)

We propose a general procedure to determine the optimum imaging parameters (spring constant and oscillation amplitude) to obtain the optimum resolution in frequency modulation atomic force microscopy. We calculated the effective signal-to-noise ratio for various spring constants and oscillation amplitudes, based on the measurement of frequency shift and energy dissipation versus tip-sample distance curves, to find the optimum. We applied this procedure for imaging a lead phthalocyanine (PbPc) thin film on a MoS(2)(0001) substrate, and found that the optimum parameters were about 5 N/m and 20 nm, respectively. An improved signal-to-noise ratio was attained in a preliminary experiment using parameters which were close to the calculated optimum.