gebhart/patrepeval huggingface dataset:
Inosine incorporation in GC rich RNA probes increases hybridization sequence specificity (1988)

Journal Article Inosine incorporation in GC rich RNA probes increases hybridization sequence specificity Get access Umesh Varshney, Umesh Varshney Search for other works by this author on: Oxford Academic PubMed Google Scholar Nadia Jahroudi, Nadia Jahroudi 1Departments of Biological Sciences, University of CalgaryCalgary, Alberta, T2N 4N1, Canada Search for other works by this author on: Oxford Academic PubMed Google Scholar J.H. van de Sande, J.H. van de Sande Search for other works by this author on: Oxford Academic PubMed Google Scholar L. Gedamu L. Gedamu 1Departments of Biological Sciences, University of CalgaryCalgary, Alberta, T2N 4N1, Canada Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 16, Issue 9, 11 May 1988, Page 4162, https://doi.org/10.1093/nar/16.9.4162 Published: 11 May 1988 Article history Accepted: 23 March 1988 Published: 11 May 1988
Nosocomial Infections in Combined Medical-Surgical Intensive Care Units in the United States (2000)

Nosocomial infections in MS ICUs at the most frequent infection sites (bloodstream, urinary, and respiratory tract) almost always were associated with use of an invasive device. Device-associated infection rates were the best available comparative rates between combined MS ICUs, but the distribution of device-associated rates should be stratified by a hospital's major teaching affiliation status.
Optimizing Polyethylenimine-Based Gene Transfer into Mammalian Brain for Analysis of Promoter Regulation and Protein Function (2003)

The efficient and safe introduction of genes into the central nervous system (CNS) is a difficult, yet much sought after objective. Two broad classes of aims can be distinguished. On the one hand, there is therapy in which the ultimate target will be the modification of an endogenous gene by homologous recombination or the remedial addition of a gene coding for a deficient protein. On the other hand, there are analytical approaches in which the aim may be either to determine the physiological relevance of a given protein by blocking or by bolstering its expression, or to dissect the regulatory mechanisms impinging on promoter function in an integrated setting. Furthermore, analysis of promoter regulation will be a prerequisite for creating constructs with optimized regulatory sequences for expressing therapeutic proteins in physiologically appropriate conditions. Microinjection of different permutations of a specific promoter into defined brain regions is a rapid and inexpensive method for assessing function and for mapping transcriptional regulatory elements. Indeed, using somatic gene transfer can provide results that otherwise could only be obtained by labor-intensive germinal transgenosis, an approach that also requires a great deal of organizational prowess and expense for maintenance of the numerous lines created.
Precision tests of quantum hall effect device DC equivalent circuit using double-series and triple-series connections (1995)

Precision tests verify the dc equivalent circuit used by Ricketts and Kemeny to describe a quantum Hall effect device in terms of electrical circuit elements. The tests employ the use of cryogenic current comparators and the double-series and triple-series connection techniques of Delahaye. Verification of the dc equivalent circuit in double-series and triple-series connections is a necessary step in developing the ac quantum Hall effect as an intrinsic standard of resistance.
Fundamental mode spot-size measurement in single-mode optical fibres (1981)

We report a very simple method for measuring the mode spot size in single-mode fibres on the same apparatus as used for attenuation measurements without additional fibre handling. Measurements as a function of wavelength lead to the equivalent step index parameters allowing one to predict directly the splice, microbending and curvature losses.
Herpes Simplex Virus: Propagation, Quantification, and Storage (2005)

Herpes simplex virus (HSV) is the prototype of a family of large, enveloped, double-stranded DNA viruses, the Herpesviridae, which cause significant morbidity and mortality in humans. Productive replication of HSV in cells in culture results in definitive changes in cellular physiology and metabolism, ultimately leading to lysis. These definitive aspects of viral-host interactions enable diagnosis of HSV infections. In this unit, a series of methods are described for the propagation, quantification, and storage of HSV. Infectious center assays are used to measure the titers of HSV stocks. In addition, immunological methods are described for documenting the accumulation of viral polypeptides in infected whole cell extracts, as well as in situ using indirect immunofluorescence. These techniques should be beneficial to basic research virologists utilizing standard laboratory HSV strains, as well as clinical microbiologists interested in characterizing HSV isolated from patients.
Oligomerization of adenosin‐5′‐<i>O</i>‐ylmethylphosphonate, an isopolar AMP analogue: Evaluation of the route to short oligoadenylates (2009)

In an attempt to prepare a library of short oligoadenylate analogues featuring both the enzyme-stable internucleotide linkage and the 5'-O-methylphosphonate moiety and thus obtain a pool of potential RNase L agonists/antagonists, we studied the spontaneous polycondensation of the adenosin-5'-O-ylmethylphosphonic acid (p(c)A), an isopolar AMP analogue, and its imidazolide derivatives employing N,N'-dicyclohexylcarbodiimide under nonaqueous conditions and uranyl ions under aqueous conditions, respectively. The RP LC-MS analyses of the reaction mixtures per se, and those obtained after the periodate treatment, along with analyses and separations by capillary zone electrophoresis, allowed us to characterize major linear and cyclic oligoadenylates obtained. The structure of selected compounds was supported, after their isolation, by NMR spectroscopy. Ab initio calculation of the model structures simulating the AMP-imidazolide and p(c)A-imidazolide offered the explanation why the latter compound exerted, in contrast to AMP-imidazolide, a very low stability in aqueous solutions.
NG-Test Carba 5 for Rapid Detection of Carbapenemase-Producing Enterobacterales from Positive Blood Cultures (2019)

The immunochromatographic assay, NG-test Carba 5 (NG Biotech), has been evaluated for detection of carbapenemase-producing <i>Enterobacterales</i> (CPE) from spiked blood cultures (<i>n</i> = 205). It detected and discriminated in less than 30 minutes KPC, IMP, VIM, NDM, and OXA-48-like producers with a sensitivity and specificity of 97.7% and 96.1%, respectively. Thus, it might help the rapid optimization of treatment of bloodstream infections due to CPE.
An Introduction to Electrochemical Methods in Neuroscience (2006)

Electrochemical methods comprise a collection of extremely useful measurement tools for neuroscience. A central feature of these methods is an electrode that provides a surface or interface where some form of a charge-transfer process occurs. This charge-transfer process gives rise to potentials and/or currents that can be measured and related either by theory or by calibration to the concentration of substances in the solution that bathes the electrode. Broadly speaking, these methods can be divided into two groups: measurements that do not involve current, known generally as potentiometric methods, and measurements that involve current flow at an electrode under potential control, known as amperometry, voltammetry, or polarography, depending upon the details of the experimental design. Amperometric and voltammetric methods are the main, but not exclusive, focus of this book. It is completely natural that neuroscientists should find electrochemical methods of value because the nervous system contains numerous electrochemically detectable targets including simple inorganic ions, catecholamine and indolamine neurotransmitters and their metabolites, glutamate, nitric oxide (NO), glucose, lactate, ascorbate, urate, hydrogen peroxide (H2O2), oxygen (O2), and pH. Moreover, the high ionic strength of biological environments creates a perfect milieu for electrochemistry, which requires conductive media.This chapter briefly introduces the history of amperometry and voltammetry in the neurosciences and briefly surveys their applications. Although not intended as a thorough explanation of the methods themselves, the chapter provides a tutorial and primer on their basic operating principles and points the interested reader to sources of more detailed information.
A Molecular Basis of Analgesic Tolerance to Cannabinoids (2007)

Clinical usage of cannabinoids in chronic pain states is limited by their central side effects and the pharmacodynamic tolerance that sets in after repeated dosage. Analgesic tolerance to cannabinoids in vivo could be caused by agonist-induced downregulation and intracellular trafficking of cannabinoid receptors, but little is known about the molecular mechanisms involved. We show here that the type 1 cannabinoid receptor (CB1) interacts physically with G-protein-associated sorting protein 1 (GASP1), a protein that sorts receptors in lysosomal compartments destined for degradation. CB1-GASP1 interaction was observed to be required for agonist-induced downregulation of CB1 in spinal neurons ex vivo as well as in vivo. Importantly, uncoupling CB1 from GASP1 in mice in vivo abrogated tolerance toward cannabinoid-induced analgesia. These results suggest that GASP1 is a key regulator of the fate of CB1 after agonist exposure in the nervous system and critically determines analgesic tolerance to cannabinoids.
Unsupervised Classification with Non-Gaussian Mixture Models Using ICA (1998)

We present an unsupervised classification algorithm based on an ICA mixture model. The ICA mixture model assumes that the observed data can be categorized into several mutually exclusive data classes in which the components in each class are generated by a linear mixture of independent sources. The algorithm finds the independent sources, the mixing matrix for each class and also computes the class membership probability for each data point. This approach extends the Gaussian mixture model so that the classes can have non-Gaussian structure. We demonstrate that this method can learn efficient codes to represent images of natural scenes and text. The learned classes of basis functions yield a better approximation of the underlying distributions of the data, and thus can provide greater coding efficiency. We believe that this method is well suited to modeling structure in high-dimensional data and has many potential applications. 1 Introduction Recently, Blind Source Separation (BSS) by...
Electrochemical growth and resistive switching of flat-surfaced and (111)-oriented Cu2O films (2009)

Flat-surfaced and fully (111)-oriented Cu2O films were grown through a chelate-assisted electrochemical approach. Based on key roles of chelating agent, the flat surface of films controlled over the columnar-grained growth was obtainable with a root-mean-square roughness value below 3 nm. Cu2O films treated by a rapid-thermal-annealing process at 200 °C exhibited unipolar switching I-V characteristics, presenting the bistable resistance states with a high resistance ratio (Roff/Ron) over 3 orders of magnitude and considerably stable switching properties within 100 switching cycles.
High perpendicular coercive field of (100)-oriented CoFe2O4 thin films on Si (100) with MgO buffer layer (2008)

CoFe 2 O 4 thin films with large perpendicular magnetic anisotropy were obtained by pulsed laser deposition on Si(100) substrates with MgO buffer layers. Transmission electron microscopy study reveals the columnar structure of these CoFe2O4 films and confirms their (100) texture. Magnetic properties of these films have been investigated in the function of substrate temperature and film thickness. A perpendicular coercivity as high as 7.8 kOe has been achieved in the CoFe2O4 film deposited at 700 °C, with a thickness of 50 nm and a grain size of 30 nm. The high coercivity mechanism is possibly associated with the magnetocrystalline anisotropy, the strain anisotropy, the shape anisotropy due to the columnar structure, and also the appropriate grain size approaching the single-domain critical value.
Regulation of adenosine 3‘:5‘-monophosphate efflux from animal cells (1978)

Cyclic AMP efflux was measured following hormonal stimulation of adenylate cyclase in a variety of animal cells including C-6 rat glioma cells, WI-38 human fibroblasts, and avian erythrocytes. Using a variety inhibitors of mitochondrial function and glycolysis, a correlation was noted between cellular ATP levels and the rate of cyclic AMP efflux in all cells examined. A relationship between the efflux rate and the magnitude of the membrane potential was not observed. Pharmacological agents which inhibited cyclic AMP egress in these cells without reducing ATP levels included several prostaglandins (A greater than B greater than E greater than F) and probenecid. The characteristics of the cyclic AMP efflux system resemble those of the organic anion transport system.
Detection of blob objects in microscopic zebrafish images based on gradient vector diffusion (2007)

The zebrafish has become an important vertebrate animal model for the study of developmental biology, functional genomics, and disease mechanisms. It is also being used for drug discovery. Computerized detection of blob objects has been one of the important tasks in quantitative phenotyping of zebrafish. We present a new automated method that is able to detect blob objects, such as nuclei or cells in microscopic zebrafish images. This method is composed of three key steps. The first step is to produce a diffused gradient vector field by a physical elastic deformable model. In the second step, the flux image is computed on the diffused gradient vector field. The third step performs thresholding and nonmaximum suppression based on the flux image. We report the validation and experimental results of this method using zebrafish image datasets from three independent research labs. Both sensitivity and specificity of this method are over 90%. This method is able to differentiate closely juxtaposed or connected blob objects, with high sensitivity and specificity in different situations. It is characterized by a good, consistent performance in blob object detection.
Separation of Shells from Walnut Meats Using Magnetic Methods (1984)

ABSTRACT THE purpose of this research was to study the feasibihty of using iron powder and magnetic fluid to remove shells from walnut meats. Privately developed methods and equipment, utilizing nontoxic glue and iron powder, were used to coat whole walnuts with iron powder. Alternately, a 1:1 mixture, consisting of 125 mL of water and 125 mL of magnetic fluid with 10 g nontoxic gelatin powder, was used to coat walnuts for the magnetic fluid treatment. Coated (both iron powder and magnetic fluid) nuts were cracked in a commercial nut cracker. Treatments were repHcated five times. Control walnuts were not treated with iron powder or magnetic fluid. Cracked walnuts (including the control) were conditioned over the permanent magnetic drum separator two times. Analyses were done to determine percentage shells and membranes removed along with percentage walnut meats recovered. Iron analyses were carried out on walnut meats. Both iron powder and magnetic fluid removed essentially all shells from walnut meats. However, both require Food and Drug Administration approval as food additives.
Distinct Roles of Ser-764 and Lys-773 at the N Terminus of von Willebrand Factor in Complex Assembly with Coagulation Factor VIII (2012)

Complex formation between coagulation factor VIII (FVIII) and von Willebrand factor (VWF) is of critical importance to protect FVIII from rapid in vivo clearance and degradation. We have now employed a chemical footprinting approach to identify regions on VWF involved in FVIII binding. To this end, lysine amino acid residues of VWF were chemically modified in the presence of FVIII or activated FVIII, which does not bind VWF. Nano-LC-MS analysis showed that the lysine residues of almost all identified VWF peptides were not differentially modified upon incubation of VWF with FVIII or activated FVIII. However, Lys-773 of peptide Ser-766-Leu-774 was protected from chemical modification in the presence of FVIII. In addition, peptide Ser-764-Arg-782, which comprises the first 19 amino acid residues of mature VWF, showed a differential modification of both Lys-773 and the α-amino group of Ser-764. To verify the role of Lys-773 and the N-terminal Ser-764 in FVIII binding, we employed VWF variants in which either Lys-773 or Ser-764 was replaced with Ala. Surface plasmon resonance analysis and competition studies revealed that VWF(K773A) exhibited reduced binding to FVIII and the FVIII light chain, which harbors the VWF-binding site. In contrast, VWF(S764A) revealed more effective binding to FVIII and the FVIII light chain compared with WT VWF. The results of our study show that the N terminus of VWF is critical for the interaction with FVIII and that Ser-764 and Lys-773 have opposite roles in the binding mechanism.
Tests of statistical hypotheses concerning several parameters when the number of observations is large (1943)

Table of contents 1. Introduction.426 2. Assumptions on the density function/(x, 6).428 3. The joint limit distribution of 0".429 4. Reduction of the general problem to the case of a multivariate normal distribution. .433 5. Tests of simple hypotheses which have uniformly best average power over a family of surfaces.445 6. Tests of simple hypotheses which have best constant power on a family of surfaces. . .450 7. Most stringent tests of simple hypotheses.451 8. Definitions of "best" tests of composite hypotheses.453 9. Tests of linear composite hypotheses which have uniformly best average power over a family of surfaces.455 10.Tests of linear composite hypotheses which have best constant power on a family of surfaces.461 11.Most stringent tests of linear composite hypotheses.461 12.The general composite hypothesis.463 13.Optimum properties of the likelihood ratio test.470 14.Large sample distribution of the likelihood ratio.478 15.
Gram-positive three-component antimicrobial peptide-sensing system (2007)

To survive during colonization or infection of the human body, microorganisms must circumvent mechanisms of innate host defense. Antimicrobial peptides represent a key component of innate host defense, especially in phagocytes and on epithelial surfaces. However, it is not known how the clinically important group of Gram-positive bacteria sense antimicrobial peptides to coordinate a directed defensive response. By determining the genome-wide gene regulatory response to human beta-defensin 3 in the nosocomial pathogen Staphylococcus epidermidis, we discovered an antimicrobial peptide sensor system that controls major specific resistance mechanisms of Gram-positive bacteria and is unrelated to the Gram-negative PhoP/PhoQ system. It contains a classical two-component signal transducer and an unusual third protein, all of which are indispensable for signal transduction and antimicrobial peptide resistance. Furthermore, our data indicate that a very short, extracellular loop with a high density of negative charges in the sensor protein is responsible for antimicrobial peptide binding and the observed specificity for cationic antimicrobial peptides. Our study shows that Gram-positive bacteria have developed an efficient and unique way of controlling resistance mechanisms to antimicrobial peptides, which may provide a promising target for antimicrobial drug development.
One-shot learning and generation of dexterous grasps for novel objects (2015)

This paper presents a method for one-shot learning of dexterous grasps and grasp generation for novel objects. A model of each grasp type is learned from a single kinesthetic demonstration and several types are taught. These models are used to select and generate grasps for unfamiliar objects. Both the learning and generation stages use an incomplete point cloud from a depth camera, so no prior model of an object shape is used. The learned model is a product of experts, in which experts are of two types. The first type is a contact model and is a density over the pose of a single hand link relative to the local object surface. The second type is the hand-configuration model and is a density over the whole-hand configuration. Grasp generation for an unfamiliar object optimizes the product of these two model types, generating thousands of grasp candidates in under 30 seconds. The method is robust to incomplete data at both training and testing stages. When several grasp types are considered the method selects the highest-likelihood grasp across all the types. In an experiment, the training set consisted of five different grasps and the test set of 45 previously unseen objects. The success rate of the first-choice grasp is 84.4% or 77.7% if seven views or a single view of the test object are taken, respectively.
Update on terbinafine with a focus on dermatophytoses (2009)

Since terbinafine was introduced on the world market 17 years ago, it has become the leading antifungal for the treatment of superficial fungal infections, aided by unique pharmacologic and microbiologic profiles. This article reviews mode of action, antimycotic spectrum and disposition profile of terbinafine. It examines the data, accumulated over 15 years, on the comparative efficacy of terbinafine (vs griseofulvin, itraconazole, fluconazole) in the management of the infections for which it is primarily indicated (eg, dermatophytoses) and provides a brief discussion on its use for the treatment of non-dermatophyte infections. Finally, the available data on the newest topical and systemic formulations are introduced.
Auto mixed light for RGB LED backlight module (2009)

To prevent the output white light from being experienced with color deviation due to temperature effect on the performance of light-emitting diode (LED), a mixed-light control module is developed, by integrating Programmable System on Chip (PSoC) with photo-diode sensor devices, to examine the ambient temperature and feedback voltage level of RGB photodiodes. Also, a mixing light color criterion of RGB LED is applied on the mixed-light control module. Through the usage of mixing light color criterion of RGB LED, the corresponding duty cycle of RGB LED can be adjusted, and the stable white light output can, consequently, be achieved. By the feedback compensation of mixed-light control module the CIE1931 xy coordinates of output light are in good agreement with the predicted results.
Layer-by-Layer Assembly of PEDOT/Polyaniline Electrochromic Devices (2001)

A fully functional switchable chromic device (see Figure) in which complementary coloration is achieved from electrostatically assembled films containing poly(aniline) (PANI) and poly(3,4-ethylenedioxythiophene) (PEDOT) is demonstrated. The color changes accompanying doping and undoping are reversible and present true optical contrast.
Adaptive granularity memory systems (2011)

We propose adaptive granularity to combine the best of fine-grained and coarse-grained memory accesses. We augment virtual memory to allow each page to specify its preferred granularity of access based on spatial locality and error-tolerance tradeoffs. We use sector caches and sub-ranked memory systems to implement adaptive granularity. We also show how to incorporate adaptive granularity into memory access scheduling. We evaluate our architecture with and without ECC using memory intensive benchmarks from the SPEC, Olden, PARSEC, SPLASH2, and HPCS benchmark suites and micro-benchmarks. The evaluation shows that performance is improved by 61% without ECC and 44% with ECC in memory-intensive applications, while the reduction in memory power consumption (29% without ECC and 14% with ECC) and traffic (78% without ECC and 66% with ECC) is significant.