gebhart/patrepeval huggingface dataset:
VirtualTaste: a web server for the prediction of organoleptic properties of chemical compounds (2021)

Taste is one of the crucial organoleptic properties involved in the perception of food by humans. Taste of a chemical compound present in food stimulates us to take in food and avoid poisons. Bitter taste of drugs presents compliance problems and early flagging of potential bitterness of a drug candidate may help with its further development. Similarly, the taste of chemicals present in food is important for evaluation of food quality in the industry. In this work, we have implemented machine learning models to predict three different taste endpoints-sweet, bitter and sour. The VirtualTaste models achieved an overall accuracy of 90% and an AUC of 0.98 in 10-fold cross-validation and in an independent test set. The web server takes a two-dimensional chemical structure as input and reports the chemical's taste profile for three tastes-using molecular fingerprints along with confidence scores, including information on similar compounds with known activity from the training set and an overall radar chart. Additionally, insights into 25 bitter receptors are also provided via target prediction for the predicted bitter compounds. VirtualTaste, to the best of our knowledge, is the first freely available web-based platform for the prediction of three different tastes of compounds. It is accessible via http://virtualtaste.charite.de/VirtualTaste/without any login requirements and is free to use.
Visual-tactile sensory map calibration of a biomimetic whiskered robot (2016)

We present an adaptive filter model of cerebellar function applied to the calibration of a tactile sensory map to improve the accuracy of directed movements of a robotic manipulator. This is demonstrated using a platform called Bellabot that incorporates an array of biomimetic tactile whiskers, actuated using electro-active polymer artificial muscles, a camera to provide visual error feedback, and a standard industrial robotic manipulator. The algorithm learns to accommodate imperfections in the sensory map that may be as a result of poor manufacturing tolerances or damage to the sensory array. Such an ability is an important pre-requisite for robust tactile robotic systems operating in the real-world for extended periods of time. In this work the sensory maps have been purposely distorted in order to evaluate the performance of the algorithm.
A novel Doppler frequency shift compensation algorithm for OFDM underwater acoustic communication system (2013)

With the rapid development of OFDM (Orthogonal Frequency Division Multiplexing) technology and its own advantages, this technology has been studied actively in underwater acoustic communication recently to improve the data transfer rate and reliability. For the reason of Doppler shift effect in underwater acoustic channel, eliminating Doppler effect became the key of whether the OFDM system can be successfully used in underwater acoustic communication. In this paper, a twice Doppler shift compensation algorithm was proposed, which has high compensation precision, low computational complexity and implementing easily.
Phosphodiesterase IV inhibitors as therapy for eosinophil-induced lung injury in asthma. (1994)

Asthma is a complex, multifactorial disease that is underpinned by airway inflammation. A variety of cytotoxic substances are released into the airway from infiltrating inflammatory cells, especially the eosinophil. These cytotoxic substances, including reactive oxygen metabolites, produce damage to the airway epithelium, a histologic feature of chronic asthma. Damage to the airway epithelium, in turn, is thought to be a major factor responsible for the development of airway hyperreactivity, a hallmark of asthma. One notable molecular target for novel antiasthmatic drugs is the cyclic AMP-specific phosphodiesterase (PDE) or PDE IV. This isozyme is the predominant form of cyclic nucleotide PDE activity in inflammatory cells. Thus, in view of the putative role of cyclic AMP as an inhibitory second messenger in these cells, PDE IV inhibitors have been shown to suppress inflammatory cell activity. The purpose of the present experiments was to examine the effect of the PDE IV inhibitor, R-rolipram, on three key functions of the guinea pig eosinophil: a) superoxide anion (O2-) production, b) adhesion to human umbilical vein endothelial cells (HUVECs), and c) infiltration into the airway. R-rolipram-elevated eosinophil cyclic AMP content (EC50 = 1.7 microM) and inhibited fMLP-induced O2- production in a concentration-dependent manner (IC50 = 0.3 microM). In contrast, neither siguazodan, a PDE III inhibitor, nor zaprinast, a PDE V inhibitor, had an appreciable effect. R-rolipram (30 microM) also reduced by 25 to 40% the adhesion of eosinophils to HUVECs stimulated with phorbol myristate acetate or tumor necrosis factor-alpha, particularly under conditions in which both cell types were simultaneously exposed to the PDE IV inhibitor.(ABSTRACT TRUNCATED AT 250 WORDS)
Good News and Bad News about Share Repurchases (1998)

We estimate the cross-sectional relationship between open market repurchases and accounting data for a large sample of dividend- paying and non-dividend paying firms over a twelve year period (1984-95). Consistent with the hypothesis that firms use open market repurchases to reduce the agency costs of free cash flow, we find that repurchases are positively related to proxies for free cash flow and negatively related to proxies for marginal financing costs. We also examine the extent to which management stock options influence the choice between open market repurchases and dividend payments. Because the value of management stock options--like any call option--is negatively related to expected future dividend payments, management can increase the value of its stock options by substituting share repurchases for dividend growth. We find evidence that such substitution occurs: for dividend-paying firms, share repurchases are positively related and dividend increases are negatively related to a proxy for management stock options, whereas for non-dividend-paying firms, the relationship between repurchases and options is weak and statistically insignificant.
Molecular Imaging of Bacterial Infections in vivo: The Discrimination between Infection and Inflammation (2014)

Molecular imaging by definition is the visualization of molecular and cellular processes within a given system. The modalities and reagents described here represent a diverse array spanning both pre-clinical and clinical applications. Innovations in probe design and technologies would greatly benefit therapeutic outcomes by enhancing diagnostic accuracy and assessment of acute therapy. Opportunistic pathogens continue to pose a worldwide threat, despite advancements in treatment strategies, which highlights the continued need for improved diagnostics. In this review, we present a summary of the current clinical protocol for the imaging of a suspected infection, methods currently in development to optimize this imaging process, and finally, insight into endocarditis as a model of infectious disease in immediate need of improved diagnostic methods.
Comparative timing measurements of LYSO and LFS to achieve the best time resolution for TOF-PET (2014)

There are research reports available presenting a Coincidence Time Resolution (CTR) below 150 ps; however often these measurements are made with short crystals of 3 or 5 mm in length. Such crystals have limited efficiency for the detection of the 511 keV gammas resulting from a positron annihilation, therefore are not really practical for a TOF-PET imaging device. We present our setup and measurements using 15 mm length crystals; a length we regard as reasonable for a TOF-PET scanner. We have used a new series of Silicon Photo Multipliers (SiPM) manufactured by Hamamatsu. These are the high Fill Factor (HFF) and Low Cross Talk (LCT) Multi Pixel Photon Counters (MPPC). We have compared two types of crystal, LFS (supplied by Zecotek) and two samples of LYSO (manufactured by Saint Gobain and CPI). We have obtained an excellent value of 148 ps for the Coincidence Time Resolution (CTR) with two LFS crystals (15 mm long) mounted on each side of a 22Na radioactive source with the HFF-MPPCs at 3.3 V over-voltage. This is in comparison to a CTR of 180 ps measured with the LYSO crystals.
Human pluripotent stem cell models of autism spectrum disorder: emerging frontiers, opportunities, and challenges towards neuronal networks in a dish (2013)

Autism spectrum disorder (ASD) is characterized by deficits in language development and social cognition and the manifestation of repetitive and restrictive behaviors. Despite recent major advances, our understanding of the pathophysiological mechanisms leading to ASD is limited. Although most ASD cases have unknown genetic underpinnings, animal and human cellular models of several rare, genetically defined syndromic forms of ASD have provided evidence for shared pathophysiological mechanisms that may extend to idiopathic cases. Here, we review our current knowledge of the genetic basis and molecular etiology of ASD and highlight how human pluripotent stem cell-based disease models have the potential to advance our understanding of molecular dysfunction. We summarize landmark studies in which neuronal cell populations generated from human embryonic stem cells and patient-derived induced pluripotent stem cells have served to model disease mechanisms, and we discuss recent technological advances that may ultimately allow in vitro modeling of specific human neuronal circuitry dysfunction in ASD. We propose that these advances now offer an unprecedented opportunity to help better understand ASD pathophysiology. This should ultimately enable the development of cellular models for ASD, allowing drug screening and the identification of molecular biomarkers for patient stratification.
Genetic and environmental influences on the ratio of 3′hydroxycotinine to cotinine in plasma and urine (2009)

Additive genetic factors are prominent in determining variation in plasma 3HC/COT but less so in determining variation in urine 3HC/COT.
pFSB technology enables field programmability in an ASIC environment (2002)

Describes pFSB (programmable functional system blocks) technology and cells, a field-programmable capability based on ViaLink antifuse technology that can be embedded in an ASIC chip. Fully compatible with existing high-speed ASIC processing, library cells, compilers, and design tools, pFSB cells give the user an extension of traditional ASIC technology that provides for additional value in both ASIC- and ASSP (application specific signal processor) based systems. Chips using pFSB structures, as memory, logic, or customized elements, give the designer the ability to make last-minute decisions in product design, as well as allowing the security of designs to be easily implemented. The availability of comprehensive testing and programming hardware and software results in a user environment for chips using pFSB cells that is both friendly and easily implemented. The authors present a description of the ViaLink programming element, a description of pFSB cells and how they are used, and a summary of design methodology, testing, and programming considerations.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
SoundLoc: Acoustic Method for Indoor Localization without Infrastructure (2014)

Identifying locations of occupants is beneficial to energy management in buildings. A key observation in indoor environment is that distinct functional areas are typically controlled by separate HVAC and lighting systems and room level localization is sufficient to provide a powerful tool for energy usage reduction by occupancy-based actuation of the building facilities. Based upon this observation, this paper focuses on identifying the room where a person or a mobile device is physically present. Existing room localization methods, however, require special infrastructure to annotate rooms. SoundLoc is a room-level localization system that exploits the intrinsic acoustic properties of individual rooms and obviates the needs for infrastructures. As we show in the study, rooms' acoustic properties can be characterized by Room Impulse Response (RIR). Nevertheless, obtaining precise RIRs is a time-consuming and expensive process. The main contributions of our work are the following. First, a cost-effective RIR measurement system is implemented and the Noise Adaptive Extraction of Reverberation (NAER) algorithm is developed to estimate room acoustic parameters in noisy conditions. Second, a comprehensive physical and statistical analysis of features extracted from RIRs is performed. Also, SoundLoc is evaluated using the dataset consisting of ten (10) different rooms. The overall accuracy of 97.8% achieved demonstrates the potential to be integrated into automatic mapping of building space.
Polysome shift assay for direct measurement of miRNA inhibition by anti-miRNA drugs (2015)

Anti-miRNA (anti-miR) oligonucleotide drugs are being developed to inhibit overactive miRNAs linked to disease. To help facilitate the transition from concept to clinic, new research tools are required. Here we report a novel method--miRNA Polysome Shift Assay (miPSA)--for direct measurement of miRNA engagement by anti-miR, which is more robust than conventional pharmacodynamics using downstream target gene derepression. The method takes advantage of size differences between active and inhibited miRNA complexes. Active miRNAs bind target mRNAs in high molecular weight polysome complexes, while inhibited miRNAs are sterically blocked by anti-miRs from forming this interaction. These two states can be assessed by fractionating tissue or cell lysates using differential ultracentrifugation through sucrose gradients. Accordingly, anti-miR treatment causes a specific shift of cognate miRNA from heavy to light density fractions. The magnitude of this shift is dose-responsive and maintains a linear relationship with downstream target gene derepression while providing a substantially higher dynamic window for aiding drug discovery. In contrast, we found that the commonly used 'RT-interference' approach, which assumes that inhibited miRNA is undetectable by RT-qPCR, can yield unreliable results that poorly reflect the binding stoichiometry of anti-miR to miRNA. We also demonstrate that the miPSA has additional utility in assessing anti-miR cross-reactivity with miRNAs sharing similar seed sequences.
NeuN As a Neuronal Nuclear Antigen and Neuron Differentiation Marker (2015)

The NeuN protein is localized in nuclei and perinuclear cytoplasm of most of the neurons in the central nervous system of mammals. Monoclonal antibodies to the NeuN protein have been actively used in the immunohistochemical research of neuronal differentiation to assess the functional state of neurons in norm and pathology for more than 20 years. Recently, NeuN antibodies have begun to be applied in the differential morphological diagnosis of cancer. However, the structure of the protein, which can be revealed by antibodies to NeuN, remained unknown until recently, and the functions of the protein are still not fully clear. In the present mini-review, data on NeuN accumulated so far are summarized and analyzed. Data on the structure and properties of the protein, its isoforms, intracellular localization, and hypothesized functions are reported. The application field of immunocytochemical detection of NeuN in scientific and clinical studies, as well as the difficulties in the interpretation of the obtained experimental data and their possible causes, is described in details.
Age of onset in Huntington disease: sex specific influence of apolipoprotein E genotype and normal CAG repeat length (1999)

Age of onset (AO) of Huntington disease (HD) is known to be correlated with the length of an expanded CAG repeat in the HD gene. Apolipoprotein E (APOE) genotype, in turn, is known to influence AO in Alzheimer disease, rendering the APOE gene a likely candidate to affect AO in other neurological diseases too. We therefore determined APOE genotype and normal CAG repeat length in the HD gene for 138 HD patients who were previously analysed with respect to CAG repeat length. Genotyping for APOE was performed blind to clinical information. In addition to highlighting the effect of the normal repeat length upon AO in maternally inherited HD and in male patients, we show that the APOE epsilon2epsilon3 genotype is associated with significantly earlier AO in males than in females. Such a sex difference in AO was not apparent for any of the other APOE genotypes. Our findings suggest that subtle differences in the course of the neurodegeneration in HD may allow interacting genes to exert gender specific effects upon AO.
Nutraceuticals: Potential for Chondroprotection and Molecular Targeting of Osteoarthritis (2013)

Osteoarthritis (OA) is a degenerative joint disease and a leading cause of adult disability. There is no cure for OA, and no effective treatments which arrest or slow its progression. Current pharmacologic treatments such as analgesics may improve pain relief but do not alter OA disease progression. Prolonged consumption of these drugs can result in severe adverse effects. Given the nature of OA, life-long treatment will likely be required to arrest or slow its progression. Consequently, there is an urgent need for OA disease-modifying therapies which also improve symptoms and are safe for clinical use over long periods of time. Nutraceuticals-food or food products that provide medical or health benefits, including the prevention and/or treatment of a disease-offer not only favorable safety profiles, but may exert disease- and symptom-modification effects in OA. Forty-seven percent of OA patients use alternative medications, including nutraceuticals. This review will overview the efficacy and mechanism of action of commonly used nutraceuticals, discuss recent experimental and clinical data on the effects of select nutraceuticals, such as phytoflavonoids, polyphenols, and bioflavonoids on OA, and highlight their known molecular actions and limitations of their current use. We will conclude with a proposed novel nutraceutical-based molecular targeting strategy for chondroprotection and OA treatment.
Tumor inhibitors. 119. Baccharin, a novel potent antileukemic trichothecene triepoxide from Baccharis megapotamica (1976)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTumor inhibitors. 119. Baccharin, a novel potent antileukemic trichothecene triepoxide from Baccharis megapotamicaS. Morris Kupchan, Bruce B. Jarvis, Richard G. Dailey Jr., William Bright, Robert F. Bryan, and Yoshikazu ShizuriCite this: J. Am. Chem. Soc. 1976, 98, 22, 7092–7093Publication Date (Print):October 1, 1976Publication History Published online1 May 2002Published inissue 1 October 1976https://pubs.acs.org/doi/10.1021/ja00438a066https://doi.org/10.1021/ja00438a066research-articleACS PublicationsRequest reuse permissionsArticle Views166Altmetric-Citations49LEARN 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
A Critical Review of Hydraulic Fracture Propagation in Shale Gas Reservoirs (2013)

The successful exploration and development of unconventional shale gas reservoirs was possible with advances in hydraulic fracturing and horizontal drilling. Hydraulic fracture treatments open these natural fractures and create a fracture network in gas shales. However, the fracture propagation is not fully understood as of now. A critical review of hydraulic fracture propagation in shale gas formations is presented in this paper. Effects of pertinent factors on hydraulic fracture propagation are described and discussed. The factors are classified into three categories: well completion, fracture treatment, and formation properties. Well completion factors include casing roughness, perforation friction, tortuosity, fracture reorientation, and horizontal wells. Fracture treatment parameters include fluid property change, friction due to proppant, variable injection rate, multi-phase flow, proppant transport, and multi-stage treatment. Formation properties include rock toughness, temperature and pore pressure expansion, stress anisotropy, natural fractures, Young’s modulus, and formation permeability. This review gives engineers and researchers a better understanding of fracture propagation in shale gas reservoirs. Keywords: Hydraulic fracturing, fracture propagation, shale gas reservoirs,  net pressure
Aquaporin‐4 Antibodies (<scp>NMO</scp>‐<scp>IgG</scp>) as a Serological Marker of Neuromyelitis Optica: A Critical Review of the Literature (2013)

Antibodies to aquaporin-4 (called NMO-IgG or AQP4-Ab) constitute a sensitive and highly specific serum marker of neuromyelitis optica (NMO) that can facilitate the differential diagnosis of NMO and classic multiple sclerosis. NMO-IgG/AQP4-Ab seropositive status has also important prognostic and therapeutic implications in patients with isolated longitudinally extensive myelitis (LETM) or optic neuritis (ON). In this article, we comprehensively review and critically appraise the existing literature on NMO-IgG/AQP4-Ab testing. All available immunoassays-including tissue-based (IHC), cell-based (ICC, FACS) and protein-based (RIPA, FIPA, ELISA, Western blotting) assays-and their differential advantages and disadvantages are discussed. Estimates for sensitivity, specificity, and positive and negative likelihood ratios are calculated for all published studies and accuracies of the various immunoassay techniques compared. Subgroup analyses are provided for NMO, LETM and ON, for relapsing vs. monophasic disease, and for various control groups (eg, MS vs. other controls). Numerous aspects of NMO-IgG/AQP4-Ab testing relevant for clinicians (eg, impact of antibody titers and longitudinal testing, indications for repeat testing, relevance of CSF testing and subclass analysis, NMO-IgG/AQP4-Ab in patients with rheumatic diseases) as well as technical aspects (eg, AQP4-M1 vs. AQP4-M23-based assays, intact AQP4 vs. peptide substrates, effect of storage conditions and freeze/thaw cycles) and pitfalls are discussed. Finally, recommendations for the clinical application of NMO-IgG/AQP4-Ab serology are given.
Circadian clock control of the cellular response to DNA damage (2010)

Mammalian cells possess a cell-autonomous molecular clock which controls the timing of many biochemical reactions and hence the cellular response to environmental stimuli including genotoxic stress. The clock consists of an autoregulatory transcription-translation feedback loop made up of four genes/proteins, BMal1, Clock, Cryptochrome, and Period. The circadian clock has an intrinsic period of about 24 h, and it dictates the rates of many biochemical reactions as a function of the time of the day. Recently, it has become apparent that the circadian clock plays an important role in determining the strengths of cellular responses to DNA damage including repair, checkpoints, and apoptosis. These new insights are expected to guide development of novel mechanism-based chemotherapeutic regimens.