gebhart/patrepeval huggingface dataset:
Characterization of receptors with a new negative image: Use in molecular docking and lead optimization (1998)

The characterization of receptor binding sites is an important aspect of molecular docking, molecular recognition, and the structure-based design process. This characterization can take several forms: the receptor surface itself can be delineated or described, the space adjacent to the surface can be chemically mapped, or a negative image of the protein binding region can be generated. In this report, we describe a new method of constructing a negative image through generation of a set of spheres. These spheres lie along the receptor surface, and their centers represent possible ligand atom positions. By the method in which they are constructed, these spheres carry a limited amount of energetic and chemical information in addition to their primary geometric information. We test the accuracy of the image by comparing sphere positions to the positions of bound ligand atoms and propose a figure of merit for such tests. Then, we use the spheres to orient ligands in enzyme active sites and show how they can be used to generate low scoring configurations more efficiently than other approaches that search orientation space. In addition, two novel applications of these spheres are described: they are used to help identify structural differences among families of enzymes and to suggest points for ligand modification in analog design.
<title>Surface imaging of the human body</title> (1994)

An optical surface scanner was used to digitize and model the torso of an adult female. This 3D surface scanner employs structured light and has an acquisition time of less than one second for a 0.4 X 0.4 X 0.4 meter sample volume. A female volunteer was digitized in three parts using this surface scanner: head, upper torso, and lower torso. External fiducials were used to aid in registration of the three data sets to create a complete body surface model. The fiducial point loci were sampled and entered in a least squares optimization scheme to rigidly transform (rotate and translate) the three data sets into alignment. The digitized data of each scan was converted into spline surfaces and imported into a computer graphics surface modeling package (Studio, Alias Research, Inc. Toronto, Canada). The results demonstrate whole body surface modeling with an optical surface scanner to achieve rapid complex 3D surface coverage.
An experiment to demonstrate the angular Doppler effect on laser light (1998)

Two simple and related experiments are outlined that allow the student to investigate the frequency shift experienced by a laser light beam when passing through a rotating half-wave retardation plate. The shift arises due to the energy exchange between a rotating optical element, in this case a half-wave plate, and a circularly polarized light beam. The shift is directly proportional to the rotation frequency of the optical element. The shift may be interpreted as an angular Doppler effect for light.
Relevance of the NLRP3 Inflammasome in the Pathogenesis of Chronic Liver Disease (2017)

Inflammation is a common characteristic of chronic liver disease (CLD). Inflammasomes are multiprotein complexes that can sense and recognize various exogenous and endogenous danger signals, eventually activating interleukin (IL)-1β and IL-18. The sensor component of the inflammasome system is a nucleotide-binding oligomerization domain (NOD)-like receptors (NLRs). The NLRs family pyrin domain containing 3 (NLRP3) inflammasome has been involved in the initiation and progression of CLD. However, the molecular mechanisms by which it triggers liver inflammation and damage remain unclear. Here, we focus on recent advances on the potential role of NLRP3 inflammasome activation in the progression of CLD, including viral hepatitis, non-alcoholic steatohepatitis and alcoholic liver disease, and in particular, its ability to alleviate liver inflammation in animal models. Additionally, we also discuss various pharmacological inhibitors identifying the NLRP3 inflammasome signaling cascade as novel therapeutic targets in the treatment of CLD. In summary, this review summarizes the relevance of the NLRP3 inflammasome in the initiation and progression of CLD, and provides critical targets to suppress the development of CLD in clinical management.
Seamless Automation and Integration of Machine Learning Capabilities for Big Data Analytics (2017)

The paper aims at proposing a solution for designing and developing a seamless automation and integration of machine learning capabilities for Big Data with the following requirements: 1) the ability to seamlessly handle and scale very large amount of unstructured and structured data from diversified and heterogeneous sources; 2) the ability to systematically determine the steps and procedures needed for analyzing Big Data datasets based on data characteristics, domain expert inputs, and data pre-processing component; 3) the ability to automatically select the most appropriate libraries and tools to compute and accelerate the machine learning computations; and 4) the ability to perform Big Data analytics with high learning performance, but with minimal human intervention and supervision. The whole focus is to provide a seamless automated and integrated solution which can be effectively used to analyze Big Data with highfrequency and high-dimensional features from different types of data characteristics and different application problem domains, with high accuracy, robustness, and scalability. This paper highlights the research methodologies and research activities that we propose to be conducted by the Big Data researchers and practitioners in order to develop and support seamless automation and integration of machine learning capabilities for Big Data analytics.
Knowledge-Based Question Answering (2002)

This paper describes the Webclopedia Question Answering system, in which methods to automatically learn patterns and parameterizations are combined with hand-crafted rules and concept ontologies. The source for answers is a collection of 1 million newspaper texts, distributed by NIST. In general, two kinds of knowledge are used by Webclopedia to answer questions: knowledge about language and knowledge about the world. The former is embodied both in the Information Retrieval engine that identifies likely answer sentences and the CONTEX parser that analyses the input question and candidate answers. The latter is embodied in a QA typology of some 140 nodes, a concept ontology of some 10,000 concepts, and the IR engine’s ranking algorithm that takes typical document structure into account.
Formation of Quantum Phase Slip Pairs in Superconducting Nanowires (2015)

For quantum computing to be practical, the effects of decoherence on quantum information must be minimized. Discovery of a regime in which transitions that conserve parity are much more likely to occur than those that do not opens the door to parity-based information processing proposals to protect quantum information.
Vision Analysis in Detecting Abnormal Breathing Activity in application to Diagnosis of Obstructive Sleep Apnoea (2006)

Recognizing abnormal breathing activity from body movement is a challenging task in machine vision. In this paper, we present a non-intrusive automatic video monitoring technique for detecting abnormal breathing activities and assisting in diagnosis of obstructive sleep apnoea. The proposed technique utilizes infrared video information and avoids imposing geometric or positional constraints on the patient. The technique also deals with fully or partially obscured patients' body. A continuously updated breathing activity template is built for distinguishing general body movement from breathing behavior.
Nebulizers in childhood (2000)

Nebulizers remain useful in the delivery of inhaled medication to children. However, for the delivery of drugs to children with asthma, they have been largely superseded by pressurized metered-dose inhalers used with large volume spacers. Where nebulizers are used, careful attention should be paid to optimizing delivery by selecting an appropriate nebulizer, using an adequate driving gas flow, and ensuring that the face mask or mouthpiece is used correctly. In this review the clinical indications for using nebulized therapy and evidence for not using it are discussed. The level of evidence upon which each statement is made is given, adapted from previous guidelines. Whatever the clinical evidence for the efficacy of nebulized drugs, the success of therapy will depend on selecting a device and regimen with which the patient will comply, and giving clear written guidelines for nebulizer use.
Online farming based on embedded systems and wireless sensor networks (2013)

The agricultural scenario seems to be one of the most promising application areas for WSN due to the necessity of providing the agricultural production chain in terms of precision and quality. This involves a careful system design, since requirements are very strict, battery life-time maximization, robustness, recovery strategies, network flexibility and re-configurability. This paper implements zigbee based wireless sensor network in agriculture such as monitoring of environmental conditions like weather, soil moisture content, soil temperature, soil fertility, weed detection, water level, monitoring growth of the crop, precision agriculture, automated irrigation facility and storage of agricultural products. The aim of this project is to monitor and maintain the farm from any part of the world through internet. Monitoring is done with the help of wireless sensor networks and all the control process is done with the help of the microcontrollers. Wireless cameras are used to feed live video of the farm to any part of the world. With the help of this project, modern technologies and new ideas can be implemented in the farm sector of our country. A farmer can see the real condition of his farm and also control his farm from any part of the world by logging into farming website. This makes the Indian farmers feel comfortable and reduces the risks involved in irrigation. The idea has the potential to attract entrepreneurs to invest in the agricultural sector.
Cytokine Regulation of Nitric Oxide Synthase in Mouse Retinal Pigment Epithelial Cells in Culture (1994)

Nitric oxide is an intercellular signaling molecule whose numerous functions include regulation of vascular tone, mediation of the cytotoxic effects of macrophages and potentiation of synaptic transmission. For some cellular functions, nitric oxide synthesis is mediated by the inducible form of nitric oxide synthase. We now show that cultured mouse retinal pigment epithelial cells exposed to interferon-gamma and lipopolysaccharide, express inducible nitric oxide synthase. The latter was detected immuno-cytochemically in interferon-gamma-lipopolysaccharide-treated retinal pigment epithelium using rabbit antiserum to a synthetic peptide of mouse nitric oxide synthase. Untreated cultures of retinal pigment epithelium or cultures treated with either interferon-gamma or or lipopolysaccharide alone were not immunoreactive. Induction of iNOS in gamma-interferon-lipopolysaccharide-stimulated retinal pigment epithelial cells was also evidenced by the presence of nitric oxide synthase enzyme activity in lysates of stimulated but not unstimulated retinal pigment epithelial cells. On immunoblots of lysates of stimulated murine retinal pigment epithelial cells, rabbit antiserum to iNOS recognized a 130-kDa protein which comigrated with the inducible nitric oxide synthase of macrophages and which was not detectable in lysates of unstimulated retinal pigment epithelial cells nor in lysates of cells treated with only interferon-gamma or lipopolysaccharide alone. Nitrite, a stable endproduct of NO formation by cells, was detectable in the culture supernatants after 18-24 hr of exposure to interferon-gamma and lipopolysaccharide, and continued to accumulate in a linear fashion for at least 96 hr. Treatment of cultured retinal pigment epithelium with interferon-gamma, lipopolysaccharide and either basic fibroblast growth factor or epidermal growth factor as third signals augmented inducible nitric oxide synthase expression as evidenced by intensified signals on immunoblots, enhanced accumulation of nitrite and increased iNOS enzyme activity. Conversely, when transforming growth factor-beta was present in the culture medium, gamma-interferon-LPS-induced expression of nitric oxide synthase and NO release were reduced. We conclude that interferon-gamma synergizes with lipopolysaccharide to induce synthesis of inducible nitric oxide synthase and production of nitric oxide by murine retinal pigment epithelium and that this induction can be modulated by basic fibroblast growth factor, epidermal growth factor or transforming growth factor-beta.
A Plea for Association Football (1906)

(1906). A Plea for Association Football. American Physical Education Review: Vol. 11, No. 1, pp. 1-7.
ENGINEERING COUNTERMEASURES TO REDUCE RED-LIGHT-RUNNING (2002)

Red-light-running is a significant problem throughout the United States and Texas. It is associated with frequent and severe crashes. Engineering countermeasures represent a useful means of combating the red-light-running problem because they are passively applied (in contrast to enforcement countermeasures which are considered to be overt and punitive) and are in the direct control of the agency responsible for the signal. The objective of this research project was to describe how engineering countermeasures can be used to minimize the frequency of red-light-running and associated crashes at intersections. This report documents the work performed, findings, and conclusions reached as a result of a two-year research project. During the first year, engineering countermeasures were identified and implemented at 10 intersections in five Texas cities. Before-after studies of red-light-running frequency were then conducted at each intersection. Also, the three-year crash history for each intersection was compared to its observed frequency of red-light-running. The findings from these studies indicate that the frequency of red-light-running decreases in a predictable way with decreasing approach flow rate, longer clearance path lengths, longer headways, and longer yellow interval durations. The crash data analyses indicate that right-angle crashes increase exponentially with an increasing frequency of red-light-running. Models for computing an intersection approach's red-light-running frequency and related crash rate are described. Guidelines for selecting appropriate engineering countermeasures and evaluating their performance are provided.
Specific nature of Trichomonas vaginalis parasitism of host cell surfaces (1985)

The adherence of Trichomonas vaginalis NYH 286 to host cells was evaluated by using monolayer cultures of HeLa and HEp-2 epithelial cells and human fibroblast cell lines. Saturation of sites on HeLa cells was achieved, yielding a maximal T. vaginalis NYH 286-to-cell ratio of two. The ability of radiolabeled NYH 286 to compete with unlabeled trichomonads for attachment and the time, temperature, and pH-dependent nature of host cell parasitism reinforced the idea of specific parasite-cell associations. Other trichomonal isolates (JH31A, RU375, and JHHR) were also found to adhere to cell monolayers, albeit to different degrees, and all isolates produced maximal contact-dependent HeLa cell cytotoxicity. The avirulent trichomonad, Trichomonas tenax, did not adhere to cell monolayers and did not cause host cell damage. Interestingly, parasite cytadherence was greater with HeLa and HEp-2 epithelial cells than with fibroblast cells. In addition, cytotoxicity with fibroblast cells never exceeded 20% of the level of cell killing observed for epithelial cells. Elucidation of properties of the pathogenic human trichomonads that allowed for host cell surface parasitism was also attempted. Treatment of motile T. vaginalis NYH 286 with trypsin diminished cell parasitism. Incubation of trypsinized organisms in growth medium allowed for regeneration of trichomonal adherence, and cycloheximide inhibited the regeneration of attachment. Organisms poisoned with metronidazole or iodoacetate failed to attach to host cells, and adherent trichomonads exposed to metronidazole or iodoacetate were readily released from parasitized cells. Coincubation experiments with polycationic proteins and sugars and pretreatment of parasites or cells with neuraminidase or periodate had no effect on host cell parasitism. Colchicine and cytochalasin B, however, did produce some inhibition of adherence to HeLa cells. The data suggest that metabolizing T. vaginalis adheres to host cells via parasite surface proteins in a specific receptor-ligand fashion. Furthermore, parasitism of epithelial cells appears to render this cell type more susceptible than fibroblast cell types to contact-dependent cytotoxicity.
The Azulenes. (1952)

ADVERTISEMENT RETURN TO ISSUEPREVArticleThe Azulenes.Maxwell. GordonCite this: Chem. Rev. 1952, 50, 1, 127–200Publication Date (Print):February 1, 1952Publication History Published online1 May 2002Published inissue 1 February 1952https://pubs.acs.org/doi/10.1021/cr60155a004https://doi.org/10.1021/cr60155a004research-articleACS PublicationsRequest reuse permissionsArticle Views1339Altmetric-Citations94LEARN 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
Requirements for antibacterial and hemolytic activities in the bovine neutrophil derived 13‐residue peptide indolicidin (1996)

The antimicrobial and hemolytic activities of the 13-residue peptide indolicidin (ILPWKWPWWPWRR-NH2), present in bovine neutrophils, and its analogs have been determined with a view to gaining insight into the structural roles of tryptophan and proline. Peptides where proline was replaced by alanine and tryptophan by phenylalanine showed antibacterial activities comparable to that of indolicidin. The peptides do not exhibit a strong propensity to occur in either helical or beta-sheet conformation. The peptides also do not appear to exert their activity by permeabilizing the bacterial plasma membrane unlike other endogenous antibacterial peptides. The presence of tryptophan appears to be essential for hemolytic activity as the phenylalanine analog does not exhibit any hemolytic activity.
D-Lactic Acidosis: An Underrecognized Complication of Short Bowel Syndrome (2015)

D-lactic acidosis or D-lactate encephalopathy is a rare condition that occurs primarily in individuals who have a history of short bowel syndrome. The unabsorbed carbohydrates act as a substrate for colonic bacteria to form D-lactic acid among other organic acids. The acidic pH generated as a result of D-lactate production further propagates production of D-lactic acid, hence giving rise to a vicious cycle. D-lactic acid accumulation in the blood can cause neurologic symptoms such as delirium, ataxia, and slurred speech. Diagnosis is made by a combination of clinical and laboratory data including special assays for D-lactate. Treatment includes correcting the acidosis and decreasing substrate for D-lactate such as carbohydrates in meals. In addition, antibiotics can be used to clear colonic flora. Although newer techniques for diagnosis and treatment are being developed, clinical diagnosis still holds paramount importance, as there can be many confounders in the diagnosis as will be discussed subsequently.
Maltose transport in Escherichia coli K-12: involvement of the bacteriophage lambda receptor (1975)

Mutants affected in lamB, the structural gene for phage lambda receptor, are unable to utilize maltose when it is present at low concentrations (less than or equal 10 muM). During growth in a chemostat at limiting maltose concentrations, the lamB mutants tested were selected against in the presence of the wild-type strain. Transport studies demonstrate that most lamB mutants have deficient maltose transport capacities at low maltose concentrations. When antibodies against purified phage lambda receptor are added to a wild-type strain, transport of maltose at low concentrations is significantly reduced. These results strongly suggest that the phage lambda receptor molecule is involved in maltose transport.
Rickettsia‐like organisms in the blue‐eyed plecostomus, <i>Panaque suttoni</i> (Eigenmann & Eigenmann) (1995)

Abstract. Intracytoplasmic organisms resembling rickettsia were observed in tissues of two blue‐eyed plecostoitius, Panaqae suttoni (Eigenmann & Eigenmann), a tropical freshwater fish. Gross lesions were limited to renomegaly and splenomegaly. Cytopathological and histopathological examination of the various tissues revealed numerous small, discrete, coccoid organisms in the cytoplasm of monocytes as well as tissue macrophages of the spleen, heart, kidney and sometimes liver. Transmission electron microscopy confirmed that these organisms were within membrane‐bound vacuoles and had a morphology resembling rickettsia.
Recent Advances in Research of the Distributed Parameters Control System with Moving Boundary (1993)

This paper presents a brief summary of the three development stages of investigation on the transpiration cooling and its control for aircraft, missiles and electromagnetic gun, then the control problem of the distributed parameters system with a moving boundary is derived. It introduces the mathematical model of the transpiration cooling control, its control characteristics, and the present situation of the experimental and theoretical study on this problem. This paper also describes the main study results and the existing problems. The prospective application is also reported. The major references in every developing stage are listed systematically for further study.
Optical Absorption of Blood Depends on Temperature during a 0.5 ms Laser Pulse at 586 nm (1998)

Optical properties are important parameters in port wine stain laser treatment models. In this study we investigated whether changes in blood optical properties occur during a 0.5 ms laser pulse. Blood from three volunteers was irradiated in vitro with laser pulses (radiant exposure 2–12 J cm−2, wavelength 586 nm, pulse length 0.5 ms). Reflection and transmission coefficients, measured using double integrating spheres, decreased slightly during the first part of the pulse. At 2.9 J cm−2 radiant exposure, the reflectance increased, independent of total radiant exposure of the pulse. This was caused by blood coagulation. A second sudden increase in reflection and a significant increase in transmission occurred near 6.3 J cm–2 and was accompanied by a "popping" sound, indicating rapid expansion of bubbles due to blood vaporization. A multilayered model of blood was used to fit calculated transmission coefficient curves to the measurements and determine temperature-dependent optical blood absorption. Heat diffusion was shown to be of minor importance. A 2.5-fold increase in absorption for temperatures increasing from 20 to 100°C, accurately describes transmission coefficients measured up to 2.9 J cm−2.