gebhart/patrepeval huggingface dataset:
Comparison of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) and Ciliary Beat Frequency Activation by the CFTR Modulators Genistein, VRT-532, and UC<sub>CF</sub>-152 in Primary Sinonasal Epithelial Cultures (2013)

IMPORTANCE: Pharmacologic activation of mucociliary clearance (MCC) represents an emerging therapeutic strategy for patients with chronic rhinosinusitis, even in the absence of congenital mutations of the CFTR gene. Drug discovery efforts have identified small molecules that activate the cystic fibrosis transmembrane conductance regulator (CFTR), including potentiators under development for treatment of cystic fibrosis. OBJECTIVE: To evaluate the properties of CFTR modulators and their effects on ciliary beat frequency (CBF) in human sinonasal epithelium (HSNE). DESIGN: Primary HSNE cultures (wild type and F508del/F508del) were used to compare stimulation of CFTR-mediated Cl(−) conductance and CBF by the CFTR modulators genistein, VRT-532, and UC(CF)-152. MAIN OUTCOMES AND MEASURES: Increase in CFTR-dependent anion transport and CBF. RESULTS: HSNE cultures were analyzed using pharmacologic manipulation of ion transport (change in short-circuit current [ΔI(SC)]) and high-speed digital imaging (CBF). Activation of CFTR-dependent anion transport was significantly different among agonists (P < .001), with genistein exerting the greatest effect (mean [SD] ΔI(SC), genistein, 23.1 [1.8] µA/cm(2) > VRT-532, 8.1 [1.0] µA/cm(2) > UC(CF)-152, 3.4 [1.4] µA/cm(2) > control, 0.7 [0.2] µA/cm(2); Tukey-Kramer P < .05) in the absence of forskolin. Genistein and UC(CF)-152 augmented CBF (under submerged conditions) significantly better (Tukey-Kramer P < .05) than cells treated with VRT-532 or dimethyl sulfoxide vehicle control (mean [SD] fold change over baseline, genistein, 1.63 [0.06]; UC(CF)-152, 1.56 [0.06]; VRT-532, 1.38 [0.08]; control, 1.27 [0.02]). Activation of CBF was blunted in F508del/F508del HSNE cultures. CONCLUSIONS AND RELEVANCE: The degree of CBF stimulation was not dependent on the magnitude of Cl(−) secretion, suggesting that different mechanisms of action may underlie MCC activation by these small molecule potentiators. Agents that activate both CFTR-dependent I(SC) and CBF are particularly attractive as therapeutics because they may address 2 independent pathways that contribute to deficient MCC in chronic rhinosinusitis.
Natural Infection of a Household Pet Red-Capped Mangabey ( <i>Cercocebus torquatus torquatus</i> ) with a New Simian Immunodeficiency Virus (1998)

A seroprevalence survey was conducted for simian immunodeficiency virus (SIV) antibody in household pet monkeys in Gabon. Twenty-nine monkeys representing seven species were analyzed. By using human immunodeficiency virus type 2 (HIV-2)/SIVsm, SIVmnd, and SIVagm antigens, one red-capped mangabey (RCM) (Cercocebus torquatus torquatus) was identified as harboring SIV-cross-reactive antibodies. A virus isolate, termed SIVrcm, was subsequently established from this seropositive RCM by cocultivation of its peripheral blood mononuclear cells (PBMC) with PBMC from seronegative humans or RCMs. SIVrcm was also isolated by cocultivation of CD8-depleted RCM PBMC with Molt 4 clone 8 cells but not with CEMx174 cells. The lack of growth in CEMx174 cells distinguished this new SIV from all previously reported sooty mangabey-derived viruses (SIVsm), which grow well in this cell line. SIVrcm was also successfully transmitted (cell free) to human and rhesus PBMC as well as to Molt 4 clone 8 cells. To determine the evolutionary origins of this newly identified virus, subgenomic pol (475 bp) and gag (954 bp) gene fragments were amplified from infected cell culture DNA and sequenced. The position of SIVrcm relative to those of members of the other primate lentivirus lineages was then examined in evolutionary trees constructed from deduced protein sequences. This analysis revealed significantly discordant phylogenetic positions of SIVrcm in the two genomic regions. In trees derived from partial gag sequences, SIVrcm clustered independently from all other HIV and SIV strains, consistent with a new primate lentivirus lineage. However, in trees derived from pol sequences, SIVrcm grouped with the HIV-1/SIVcpz lineage. These findings suggest that the SIVrcm genome is mosaic and possibly is the result of a recombination event involving divergent lentiviruses in the distant past. Further analysis of this and other SIVrcm isolates may shed new light on the origin of HIV-1.
Synthesis and cycloaddition reactions of fluorenethione S-benzoylimide (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and cycloaddition reactions of fluorenethione S-benzoylimideEdward M. Burgess and Harold R. PentonCite this: J. Org. Chem. 1974, 39, 19, 2885–2892Publication Date (Print):September 1, 1974Publication History Published online1 May 2002Published inissue 1 September 1974https://pubs.acs.org/doi/10.1021/jo00933a014https://doi.org/10.1021/jo00933a014research-articleACS PublicationsRequest reuse permissionsArticle Views136Altmetric-Citations36LEARN 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
Methodologies for Medical Computing. Computers for Medical Imaging and Graphics: Muscle Biopsy Data Acquisition and Display (1983)

Contemporary analysis of human or experimental muscle biopsies includes documentation of muscle fiber size for each fiber type. A semi-automated system has been devised to classify fibers, measure diameters, and display results. Special stains convert different fiber types to specific shades of gray. The microscope image is transmitted by a TV camera to a picture-processing computer. Muscle cells are recognized, classified, and measured for their minimum diameter. Data on consecutive fibers are summed and displayed as lists, histograms, or graphs according to each fiber type. Interpretation of the results is provided by the neuropathologist based on an awareness of probabilities associated with prior comparable results. Data on all patients is accumulated in categories according to disease, sex, age, and site.
Nondestructive Determination of Thickness and Refractive Index of Transparent Films (1964)

A simple nondestructive method of measuring the refractive index and thickness of transparent films on reflective substrates has been developed. The technique involves the use of a microscope equipped with a monochromatic filter on the objective and a stage that can be rotated so that the reflected light is observed at various angles. The film thickness, d, is given by d = [ΔNλ]/[2µ(cos r <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> − cos r <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</inf> )], where λ is the wavelength of the filtered light, µ is the refractive index, and ΔN is the number of fringes observed between the angles of refraction r <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> and r <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</inf> . This technique is especially suited for films thicker than one micron. Techniques are also described for obtaining accurate thicknesses of films less than one micron by the combined use of monochromatic filters and an interference pattern chart. These techniques can be used to determine film thicknesses ranging from several hundred angstroms to several microns with accuracies of 0.2% on films thicker than 2µ, and accuracies of tens of angstroms on thinner films. Since visual comparisons of color can be used fairly easily for film thickness determinations, the techniques were used to construct a color chart for thermally grown SiO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> films up to 1.5µ thick.
Thrombosis and Neointima Formation in Vein Grafts Are Inhibited by Locally Applied Aspirin Through Endothelial Protection (2004)

Vein graft failure within the first month after bypass surgery is largely because of thrombosis. However, systemic study of thrombus formation in vein grafts is still lacking, and few effective techniques are available to prevent this event. Herein, we analyzed the kinetics of thrombosis and tested the effectiveness of locally applied aspirin on prevention of the disease in a mouse model. En face analysis of vein grafts revealed that 67+/-12% and 54+/-17% of the surface areas were covered by microthrombi at 1 and 3 days, respectively. Thrombus generation was also identified by labeling of platelets and fibrin, which occurred in 35 grafts examined at 1 and 3 days and 1, 2, 4, and 8 weeks. In a fifth of grafts, the thrombus occluded the vessel lumen by > or =1/4. Furthermore, a significant loss of endothelial cells was evidenced by beta-gal staining for vein grafts in transgenic mice expressing LacZ gene controlled by TIE2-endothelial specific gene promoter. Following thrombosis, neointimal lesions were significantly increased by 4-fold 2 weeks after the operation. When vein grafts were treated locally with aspirin in pluronic gel-127, the thrombus area was significantly reduced (P<0.005) at 1, 4, and 8 weeks. Interestingly, neointimal lesions were markedly reduced in the local, but not oral, aspirin-treated group at 4 and 8 weeks by 50% to 70% (P<0.005). The mechanism of reduced lesions by locally applied aspirin involved the protection of vein graft endothelium. Thus, we provide strong evidence that thrombus formation occurs before the development of neointimal lesions in vein grafts and that local aspirin treatment successfully reduces vein graft arteriosclerosis through endothelial protection, resulting in reduction of thrombosis.
Development of an Efficient Therapeutic Agent for Alzheimer's Disease: Design and Synthesis of Dual Inhibitors of Acetylcholinesterase and Serotonin Transporter (2010)

To date, acetylcholinesterase (AChE) inhibitors have been clinically effective drugs for the palliative treatment of Alzheimer's disease, but their clinical efficacy is limited, mainly due to their adverse effects on peripheral organs. Since patients of Alzheimer's disease often exhibit depression as well as memory impairment, dual inhibitors of AChE and serotonin transporter (SERT) would be a better therapeutic method. Anti-depressive effects based on SERT inhibition would reduce the dose-related side effects of AChE inhibitors. Such dual inhibitors were designed by the hybridization of rivastigmine and fluoxetine based on a hypothetical model of the AChE active site. Various derivatives were synthesized and evaluated for their in vitro inhibition, and then (S)-5j (RS-1259), which possessed balanced inhibitory activities of AChE (IC(50)=101 nM) and SERT (IC(50)=42 nM), was successfully obtained. An ex vivo experiment in mice indicated that (S)-5j (RS-1259) simultaneously inhibited AChE and SERT in the brain following an oral administration. The simultaneous elevation of extracellular levels of acetylcholine and serotonin in the rat hippocampus was actually confirmed by microdialysis.
Gene rearrangements in the molecular pathogenesis of acute promyelocytic leukemia (1997)

Acute Promyelocytic Leukemia (APL) is a distinct subtype of myeloid leukemia that in the USA alone affects more than 3,000 individuals every year. APL is characterized by three distinct and unique features: (i) the accumulation in the bone marrow of tumor cells with promyelocytic features; (ii) the invariable association with specific translocations which always involve chromosome 17 and the Retinoic Acid Receptor α (RARα) locus; (iii) the exquisite sensitivity of APL blasts to the differentiating action of Retinoic Acid (RA). These features have led APL to become the paradigm for therapeutic approaches utilizing differentiating agents. The last 5 years have provided crucial insights into the molecular basis of APL. RARα translocates in 99% of cases to a gene located on chromosome 15 that we initially named myl and subsequently has been called PML. In a few cases, RARα variably translocates to chromosome 11 where it fuses to the PLZF gene or to a newly described partner, NuMA. In addition, RARα is also found translocated to chromosome 5 where it fuses to the NPM gene. The cloning of variant translocations in APL and the comparative analysis of their associated products is crucial for the understanding of the molecular etiopathogenesis of the disease. The generation of animal models, i.e., transgenic mice expressing the fusion genes, will be instrumental in determining the precise contribution of these fusion genes to leukemogenesis. In fact, mice harboring a PML/RARα transgene whose expression is specifically targeted to the myeloid-promyelocytic lineage develop acute myeloid leukemia with promyelocytic features. Moreover, the functional analysis of the various fusion proteins, as well as RARα partners, is revealing striking common features beneath a misleading structural heterogeneity which unravels a possible unifying molecular mechanism towards APL leukemogenesis. J. Cell. Physiol. 173:288–296, 1997. © 1997 Wiley-Liss, Inc.
Rapid Detection of Influenza A Pandemic (H1N1) 2009 Virus Neuraminidase Resistance Mutation H275Y by Real-Time Reverse Transcriptase PCR (2010)

The emergence of oseltamivir-resistant influenza A pandemic (H1N1) 2009 virus highlights the need for rapid oseltamivir resistance screening. We report the development and validation of high-throughput real-time reverse transcriptase PCR assays for the detection of the H275Y substitution in the neuraminidase 1 gene that can be accomplished in 3 to 4 h.
Spontaneous Hydrolysis of Ionized Phosphate Monoesters and Diesters and the Proficiencies of Phosphatases and Phosphodiesterases as Catalysts (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTSpontaneous Hydrolysis of Ionized Phosphate Monoesters and Diesters and the Proficiencies of Phosphatases and Phosphodiesterases as CatalystsRichard Wolfenden, Caroline Ridgway, and Gregory YoungView Author Information Department of Biochemistry and Biophysics University of North Carolina Chapel Hill, North Carolina 27599 Cite this: J. Am. Chem. Soc. 1998, 120, 4, 833–834Publication Date (Web):January 16, 1998Publication History Received25 September 1997Published online16 January 1998Published inissue 1 February 1998https://pubs.acs.org/doi/10.1021/ja9733604https://doi.org/10.1021/ja9733604rapid-communicationACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views979Altmetric-Citations117LEARN 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 SUBJECTS:Hydrolysis,Kinetic parameters,Peptides and proteins,Phosphates,Transition states Get e-Alerts
Single-piece all-solid-state ion-selective electrode (1995)

A novel concept of a single-piece all-solid-state ion-selective electrode (SPE) is introduced. A processable conjugated (electronically conducting or semiconducting) polymer (CP) is dissolved in a cocktail containing the components used for a conventional ion-selective poly(vinyl chloride) matrix membrane. The cocktail, containing the CP, is cast directly on a solid substrate (glassy carbon), resulting in a SPE. The role of the CP is to mediate the charge transfer between the substrate and the membrane. Two soluble CPs are studied: (i) poly(3-octylthiophene) in its undoped state and (ii) polyaniline doped (protonated) with bis(2-ethylhexyl) hydrogen phosphate. Experimental results obtained for lithium-selective SPEs and calcium-selective SPEs are discussed. All the SPEs studied show near-Nernstian responses, and no redox interference is observed as long as the concentration of the CP is sufficiently low. The incorporation of a CP, particularly polyaniline, in the membrane is shown to improve the stability of the standard potential of the SPE compared to the corresponding coated-wire electrode (membrane without CP). Impedance measurements provide information about the charge transfer processes of the electrodes.
Analyzing the performance of NoSQL vs. SQL databases for Spatial and Aggregate queries (2017)

Relational databases have been around for a long time and spatial databases have exploited this feature for close to two decades. The recent past has seen the development of NoSQL non-relational databases, which are now being adopted for spatial object storage and handling, too. While SQL databases face scalability and agility challenges and fail to take the advantage of the cheap memory and processing power available these days, NoSQL databases can handle the rise in the data storage and frequency at which it is accessed and processed - which are essential features needed in geospatial scenarios, which do not deal with a fixed schema(geometry) and fixed data size. This paper attempts to evaluate the performance of an existing NoSQL database 'MongoDB' with its inbuilt spatial functions with that of a SQL database with spatial extension 'PostGIS' for two problems – spatial and aggregate queries, across a range of datasets, with varying features counts. All the data in the analysis was processed In-memory and no secondary memory was used. Initial results suggest that MongoDB performs better by an average factor of 10x-25x which increases exponentially as the data size increases in both indexed and non-indexed operations. Given these results, NoSQL databases may be better suited for simultaneous multiple-user query systems including Web-GIS and mobile-GIS. Further studies are required to understand the full potential of NoSQL databases across various geometries and spatial query types.
Group 2 innate lymphoid cells and <scp>CD</scp>4<sup>+</sup> T cells cooperate to mediate type 2 immune response in mice (2014)

Lung ILC2s function to promote adaptive immunity in addition to their established roles in innate immunity. This novel function of ILC2s needs to be taken into account when considering the pathophysiology of asthma and other allergic airway diseases.
Biological Effects Produced by Intense Pulsed Light (Xe-Cl) on the Cartilage of the Tongue Chick Embryo Using Various Filters (2009)

The Laser used correctly in the medical practice offers clear advantages compared with traditional therapies. The improvement and even the elimination of many significant skin lesions can be achieved with reduced risks to patients. However, it is important to keep security measures and understand the possible effects on an experimental model. The chick embryo is a good model to evaluate the direct effects of non-ionizing radiation for its easy handling and availability. The purpose of this communication is to show our histological findings in organs of the chick embryo with and without protective barrier to be subjected to radiation excimer. We used the following issuers: intense pulsed light (excimer Xe-Cl laser of 308 nm wavelength). It was irradiated embryos through an open window on eggshells. Aseptically the eggs were kept for 24 hours in an incubator. The protective barriers were used with and without colored glass, latex, cellophane, paper, polycarbonate of different colors and thicknesses. The most outstanding results, with no barrier and barriers with transparent and green were intense marked congestion in capillaries, edema and focus the necrosis. We concluded that the tissue changes observed are consistent with possible side effects of these radiations fototrmicos we warned about possible side effects when they are applied indiscriminately. We believe it is important to explore different means to safeguard the safety of operators and patients.
<scp>Robula+</scp>: an algorithm for generating robust XPath locators for web testing (2016)

Automated test scripts are used with success in many web development projects, so as to automatically verify key functionalities of the web application under test, reveal possible regressions and run a large number of tests in short time. However, the adoption of automated web testing brings advantages but also novel problems, among which the test code fragility problem. During the evolution of the web application, existing test code may easily break and testers have to correct it. In the context of automated DOM-based web testing, one of the major costs for evolving the test code is the manual effort necessary to repair broken web page element locators – lines of source code identifying the web elements (e.g. form fields and buttons) to interact with. In this work, we present Robula+, a novel algorithm able to generate robust XPath-based locators – locators that are likely to work correctly on new releases of the web application. We compared Robula+ with several state of the practice/art XPath locator generator tools/algorithms. Results show that XPath locators produced by Robula+ are by far the most robust. Indeed, Robula+ reduces the locators' fragility on average by 90% w.r.t. absolute locators and by 63% w.r.t. Selenium IDE locators. Copyright © 2016 John Wiley & Sons, Ltd.
Having a BLAST with bioinformatics (and avoiding BLASTphemy) (2001)

Searching for similarities between biological sequences is the principal means by which bioinformatics contributes to our understanding of biology. Of the various informatics tools developed to accomplish this task, the most widely used is BLAST, the basic local alignment search tool. This article discusses the principles, workings, applications and potential pitfalls of BLAST, focusing on the implementation developed at the National Center for Biotechnology Information.