gebhart/patrepeval huggingface dataset:
Kinetics and Mechanism of ATP-Dependent IL-1β Release from Microglial Cells (2000)

Endotoxin-dependent release of IL-1 beta from mouse microglial cells is a very inefficient process, as it is slow and leads to accumulation of a modest amount of extracellular cytokine. Furthermore, secreted IL-1 beta is mostly in the procytokine unprocessed form. Addition of extracellular ATP to LPS-primed microglia caused a burst of release of a large amount of processed IL-1 beta. ATP had no effect on the accumulation of intracellular pro-IL-1 beta in the absence of LPS. In LPS-treated cells, ATP slightly increased the synthesis of pro-IL-1 beta. Optimal ATP concentration for IL-1 beta secretion was between 3 and 5 mM, but significant release could be observed at concentrations as low as 1 mM. At all ATP concentrations IL-1 beta release could be inhibited by increasing the extracellular K+ concentration. ATP-dependent IL-1 beta release was also inhibited by 90 and 60% by the caspase inhibitors YVAD and DEVD, respectively. Accordingly, in ATP-stimulated microglia, the p20 proteolytic fragment derived from activation of the IL-1-beta-converting enzyme could be detected by immunoblot analysis. These experiments show that in mouse microglial cells extracellular ATP triggers fast maturation and release of intracellularly accumulated IL-beta by activating the IL-1-beta-converting enzyme/caspase 1.
Neural Stimulation and Recording with Bidirectional, Soft Carbon Nanotube Fiber Microelectrodes (2015)

The development of microelectrodes capable of safely stimulating and recording neural activity is a critical step in the design of many prosthetic devices, brain-machine interfaces, and therapies for neurologic or nervous-system-mediated disorders. Metal electrodes are inadequate prospects for the miniaturization needed to attain neuronal-scale stimulation and recording because of their poor electrochemical properties, high stiffness, and propensity to fail due to bending fatigue. Here we demonstrate neural recording and stimulation using carbon nanotube (CNT) fiber electrodes. In vitro characterization shows that the tissue contact impedance of CNT fibers is remarkably lower than that of state-of-the-art metal electrodes, making them suitable for recording single-neuron activity without additional surface treatments. In vivo chronic studies in parkinsonian rodents show that CNT fiber microelectrodes stimulate neurons as effectively as metal electrodes with 10 times larger surface area, while eliciting a significantly reduced inflammatory response. The same CNT fiber microelectrodes can record neural activity for weeks, paving the way for the development of novel multifunctional and dynamic neural interfaces with long-term stability.
Formation of a Polymer-Protected Platinum Sol: A New Understanding of the Parameters Controlling Morphology (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFormation of a Polymer-Protected Platinum Sol: A New Understanding of the Parameters Controlling MorphologyDaniel G. Duff, Peter P. Edwards, and Brian F. G. JohnsonCite this: J. Phys. Chem. 1995, 99, 43, 15934–15944Publication Date (Print):October 1, 1995Publication History Published online1 May 2002Published inissue 1 October 1995https://pubs.acs.org/doi/10.1021/j100043a036https://doi.org/10.1021/j100043a036research-articleACS PublicationsRequest reuse permissionsArticle Views1146Altmetric-Citations149LEARN 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 options Get e-Alerts
Fuzzy vector median-based surface smoothing (2004)

This paper proposes a novel approach for smoothing surfaces represented by triangular meshes. The proposed method is a two-step procedure: surface normal smoothing through fuzzy vector median (FVM) filtering followed by integration of surface normals for vertex position update based on the least square error (LSE) criteria. Median and Order Statistic-based filters are extensively used in signal processing, especially image processing, due to their ability to reject outliers and preserve features such as edges and monotonic regions. More recently, fuzzy ordering theory has been introduced to allow averaging among similarly valued samples. Fuzzy ordering theory leads naturally to the fuzzy median, which yields improved noise smoothing over traditional crisp median filters. This paper extends the fuzzy ordering concept to vector-based data and introduces the fuzzy vector median filter. The application of FVM filters to surface normal smoothing yields improved results over previously introduced normal smoothing algorithms. The improved filtering results, coupled with LSE vertex position update, produces surface smoothing that minimizes the effects of noise while simultaneously preserving detail features. The proposed method is simple to implement and relatively fast. Simulation results are presented showing the performance of the proposed method and its advantages over commonly used surface smoothing algorithms. Additionally, optimization procedures for FVM filters are derived and evaluated.
Wearable speech enhancement system based on MEMS microphone array for disabled people (2015)

Disabled people, especially the ones with motor skill impairments, have difficulties in interacting with personal computers and smartphones. Indeed Automatic Speech Recognition (ASR) could be helpful for those people, but it's limited in scenarios not affected by environmental noise that can decrease performance of the recognition, limiting user experience. We propose a speech enhancement system based on MEMS microphone array and a digital signal processor in order to increase signal-to-noise ratio (SNR) of the user's voice. The audio delay between microphones is exploited by the array using the Differential Microphone Array (DMA) and an Adaptive Noise Reduction techniques. In such way the system can obtain an increment in SNR about 16.5 dB, when noise and voice come from opposite directions. A voice activity detection (VAD) block recognizes when the user speaks and sends the data to a cloud-based ASR system. Due to the small array size, the embedded system can be integrated in a wearable device. Theoretical analysis and in-system measurements prove the effectiveness of the proposed solution.
Cough in Tetraplegic Subjects: An Active Process (1990)

In tetraplegic subjects the clavicular portion of the pectoralis major plays a major role during coughing. Its contraction causes a reduction in the size of the upper part of the rib cage and a rise in intrathoracic pressure; this pressure rise results secondarily in an outward (paradoxical) motion of the abdomen and the lower rib cage. Cough in tetraplegic subjects is thus an active, rather than a passive, process, and its effectiveness might be improved by a combination of specific muscle training and abdominal binding.
[Not Available]. (2012)

﻿﻿﻿﻿﻿﻿ An important part of the wound healing process is the removal of necrotic tissue from a wound to promote healing. Enzymatic de- bridement is one of the widely used methods to accomplish this goal. Clostridium collagenase (C. collagenase) containing ointment is fre- quently used in clinics to debride wounds. In this work, the influence of metal salts and various types of surfactants on the enzymatic activ- ity of C. collagenase is tested. The relationship between charge and size of metal ions and surfactant structure is explained in the context of enzyme inhibition. Commonly used wound care products, such as cleansers, dressings, antimicrobial formulations, and silver dressings are tested with C. collagenase. The results are discussed in terms of enzyme compatibility with such materials, and recommendations for use of wound care accessories in conjunction with the debriding en- zyme are given, with the aim to help wound care providers make more educated choices towards accomplishing optimal therapy outcome. ﻿﻿﻿.
Use of restriction fragment length polymorphism as a genetic marker for typing Mycobacterium avium strains (1995)

Restriction fragment length polymorphism (RFLP) was used to study 75 clinical isolates identified as Mycobacterium avium. Two repetitive insertion sequences, IS1311 and IS900, were used as DNA probes. Although less than 25% of isolates showed RFLP patterns with IS900, all strains gave banding patterns with IS1311. M. avium strains isolated from patients with AIDS exhibited marked polymorphism with both probes.
Adenylate cyclase in Saccharomyces cerevisiae is a peripheral membrane protein. (1990)

The adenylate cyclase system of the yeast Saccharomyces cerevisiae contains the CYR1 polypeptide, responsible for catalyzing formation of cyclic AMP (cAMP) from ATP, and two RAS polypeptides, which mediate stimulation of cAMP synthesis of guanine nucleotides. By analogy to the mammalian enzyme, models of yeast adenylate cyclase have depicted the enzyme as a membrane protein. We have concluded that adenylate cyclase is only peripherally bound to the yeast membrane, based on the following criteria: (i) substantial activity was found in cytoplasmic fractions; (ii) activity was released from membranes by the addition of 0.5 M NaCl; (iii) in the presence of 0.5 M NaCl, activity in detergent extracts had hydrodynamic properties identical to those of cytosolic or NaCl-extracted enzyme; (iv) antibodies to yeast adenylate cyclase identified a full-length adenylate cyclase in both membrane and cytosol fractions; and (v) activity from both cytosolic fractions and NaCl extracts could be functionally reconstituted into membranes lacking adenylate cyclase activity. The binding of adenylate cyclase to the membrane may have regulatory significance; the fraction of activity associated with the membrane increased as cultures approached stationary phase. In addition, binding of adenylate cyclase to membranes appeared to be inhibited by cAMP. These results indicate the existence of a protein anchoring adenylate cyclase to the membrane. The identity of this protein remains unknown.
Molecular Mechanisms of Fragile X Syndrome: A Twenty-Year Perspective (2011)

Fragile X syndrome (FXS) is a common form of inherited intellectual disability and is one of the leading known causes of autism. The mutation responsible for FXS is a large expansion of the trinucleotide CGG repeat in the 5' untranslated region of the X-linked gene FMR1. This expansion leads to DNA methylation of FMR1 and to transcriptional silencing, which results in the absence of the gene product, FMRP, a selective messenger RNA (mRNA)-binding protein that regulates the translation of a subset of dendritic mRNAs. FMRP is critical for mGluR (metabotropic glutamate receptor)-dependent long-term depression, as well as for other forms of synaptic plasticity; its absence causes excessive and persistent protein synthesis in postsynaptic dendrites and dysregulated synaptic function. Studies continue to refine our understanding of FMRP's role in synaptic plasticity and to uncover new functions of this protein, which have illuminated therapeutic approaches for FXS.
Nucleic acid related compounds. 114. Synthesis of 2,6‐(disubstituted)purine 2′,3′‐dideoxynucleosides and selected cytotoxic, anti‐hepatitis b, and adenosine deaminase substrate activities (2001)

Abstract Selected 2,6‐(disubstituted)purine 2′,3′‐didehydro‐2′,3′‐dideoxynucleosides and 2′,3′‐dideoxynucleosides were prepared and evaluated. Treatment of 5′‐protected ribonucleosides with phenoxythiocarbonyl chloride and 4‐(dimethylamino)pyridine, or under Schotten‐Baumann conditions, gave high yields of 2′,3′‐ O ‐thiono‐carbonates that underwent Corey‐Winter elimination. Treatment of unprotected ribonucleosides with α‐ace‐toxyisobutyryl bromide in “moist” acetonitrile gave trans 2′,3′‐bromohydrin acetate mixtures that underwent reductive elimination with zinc‐copper couple or zinc/acetic acid. Catalytic hydrogenation of the resulting 2′,3′‐enes gave 2′,3′‐dideoxynucleosides. Treatment of the 2‐amino‐6‐chloropurine and 6‐amino‐2‐fluoro‐purine derivatives with nucleophiles gave 2,6‐(disubstituted)purine 2′,3′‐dideoxynucleosides. 2′,3′‐Dideoxyguanosine and the 2‐amino‐6‐[amino ( 16d ), methoxy ( 16b ), ethoxy ( 16c ), and methylamino ( 16j )]purine 2′,3′‐dideoxynucleosides showed good anti‐hepatitis B activity with infected primary duck hepatocytes. Cytotoxic effects with selected analogues were evaluated in human T‐lymphoblastic and promyelocytic leukemia cell lines. The 2‐amino‐6‐fluoro derivative 16m was the most cytotoxic of the 2‐amino‐6‐(substituted)purine 2′,3′‐dideoxynucleosides, and 2‐fluoro‐2′,3′‐dideoxyadenosine ( 21a ) was the most cytotoxic compound. The order of efficiency of hydrolysis of the 6‐substituent from 2‐amino‐6‐(sub‐stituted)purine 2′,3′‐dideoxynucleosides ( V max / K m ) with adenosine deaminase from calf intestine was: 2‐amino‐6‐[amino ( 16d ) > methoxy ( 16b ) > ethoxy ( 16c )], all of which were ≤3% of the efficiency with adenosine. The 6‐methylamino derivative 16j , as well as 16b , 16c , and 16d were readily converted into 2′,3′‐dideoxyguanosine by duck cell supernatants.
Semantic Instance Annotation of Street Scenes by 3D to 2D Label Transfer (2015)

Semantic annotations are vital for training models for object recognition, semantic segmentation or scene understanding. Unfortunately, pixelwise annotation of images at very large scale is labor-intensive and only little labeled data is available, particularly at instance level and for street scenes. In this paper, we propose to tackle this problem by lifting the semantic instance labeling task from 2D into 3D. Given reconstructions from stereo or laser data, we annotate static 3D scene elements with rough bounding primitives and develop a model which transfers this information into the image domain. We leverage our method to obtain 2D labels for a novel suburban video dataset which we have collected, resulting in 400k semantic and instance image annotations. A comparison of our method to state-of-the-art label transfer baselines reveals that 3D information enables more efficient annotation while at the same time resulting in improved accuracy and time-coherent labels.
Does metabolic radiolabeling stimulate the stress response? Gene expression profiling reveals differential cellular responses to internal beta vs. external gamma radiation (2003)

DNA microarray analyses were used to investigate the effect of cell-incorporated 35S-methionine on human colorectal carcinoma cells. This beta-radiation-induced gene expression profile was compared with that induced by external gamma-radiation. The extent of DNA fragmentation was used as a biomarker to determine the external gamma dose that was bioequivalent to that received by cells incubated in medium containing 35S-methionine. Studies showed that 35S-methionine at 100 microCi/mL induced a much more robust transcriptional response than gamma-radiation (2000 cGy) when evaluated 2 h after the labeling or irradiation period. The cellular response to internal beta-radiation was greater not only with respect to the number of genes induced, but also with respect to the level of gene induction. Not surprisingly, the induced genes overlapped with the set of gamma-responsive genes. However, a distinct beta-gene induction profile that included a large number of cell adhesion proteins was also observed. Taken together, these studies demonstrate that metabolic incorporation of a low energy beta-emitter, such as 35S-methionine, can globally influence a diverse set of cellular activities that can, in turn, affect the outcome of many experiments by altering the cell cycle, metabolic, signaling, or redox status (set point) of the cell. Additional studies of the mechanism of beta-induced proliferation arrest and cell death and of the significance of its differential gene induction/repression profile in comparison to pulsed gamma-irradiation may lead to new insights into the ways in which ionizing radiation can interact with cells.
Partial characterization of a Candida albicans fimbrial adhesin (1994)

Candida albicans is the primary etiologic agent of candidiasis, a disease that can vary from superficial mucosal lesions to life-threatening systemic or disseminated diseases. Strains of C. albicans have been reported to possess long, thin filamentous protein cell surface appendages termed fimbriae (R.B. Gardiner, M. Canton, and A. W. Day, Bot. Gaz. 143:534-541, 1982). These fimbriae were isolated, purified, and partially characterized. The major structural subunit of the fimbriae is a glycoprotein which consists of 80 to 85% carbohydrate (consisting primarily of D-mannose) and 10 to 15% protein. The molecular weight of the glycosylated fimbrial subunit is approximately 66,000, while unglycosylated protein has an approximate molecular weight of 8,644. The fimbriae function as adhesins mediating C. albicans binding to human buccal epithelial cells. Amino acid analysis of the purified fimbrial subunit indicates that the fimbrial subunit is composed of 50% hydrophobic amino acid residues. The N terminus of the fimbrial subunit is blocked to N-terminal sequencing.
Constrained imaging: overcoming the limitations of the Fourier series (1996)

Magnetic resonance imaging (MRI) is usually implemented as a Fourier transform-based technique. During data acquisition, spatially resolved information relating to spin density, relaxation rates, chemical shifts, and other parameters is phase and frequency encoded in the measured data. Image reconstruction is accomplished through the use of the Fourier series model, which can be evaluated efficiently using a fast Fourier transform (FFT) algorithm. Theoretically, the Fourier series is capable of producing perfect images if the data space (often called k-space) is sufficiently covered. In practice, several problems arise with this model due to finite sampling. Specifically, finite sampling leads to a truncation or the Fourier series, which results in image blurring and ringing. Image blurring is attributed to a loss of spatial resolution. In fact, with the Fourier series model, the resulting image resolution is limited to roughly the reciprocal of the frequency interval over which the data are sampled. The ringing artifact is due to the well-known Gibbs phenomenon, which is more pronounced for images with sharp edges. In order to overcome these limitations associated with the direct application of the Fourier series model, many alternatives have been proposed in the past decade to incorporate a priori information into the imaging process. This article discusses the constrained imaging concept. Specifically, the authors review 3 model-based imaging techniques that the authors have developed in the past few years. An essential feature of these methods is that a parametric model in the form of a generalized series is superimposed on the underlying measured data or image.
The application of functional magnetic resonance imaging and positron emission tomography in the study of anesthesia (2011)

Background The developments of functional imaging techniques, expecially of functional magnetic resonance imaging (fMRI) and positron emission tomography (PET), have provided us novel approaches for the study on the mechanisms of general anesthesia and pain. Purpose Here we summarise the use of fMRI and PET in the study of anesthesia in recent years.Content It has been shown that general anesthetics could decrease the neuronal activities in some cerebral areas (e.g. thalamus)but enchance the activitiis in some other regions (e.g. anterior cingulate cortex and insula). The special application of PET in the study of cerebral receptor system confirmed that effects of anesthetics in vivo are partially mediated through GABAergic mechanisms.The results from pain studies showed that opioid analgesics decreased the neuronal activity in the regions involved in pain perception and increased the neuronal activity in the regions related to pain modulation. Trend The evolution and the wide application of fMRI and PET surely will promote the improvement of anesthesia study.

Key words: 
fMRI;  PET;  Receptor;  Pain
Two-channel microelectrochemical bipolar electrode sensor array (2012)

We report a two-channel microelectrochemical sensor that communicates between separate sensing and reporting microchannels via one or more bipolar electrodes (BPEs). Depending on the contents of each microchannel and the voltage applied across the BPE, faradaic reactions may be activated simultaneously in both channels. As presently configured, one end of the BPE is designated as the sensing pole and the other as the reporting pole. When the sensing pole is activated by a target, electrogenerated chemiluminescence (ECL) is emitted at the reporting pole. Compared to previously reported single-channel BPE sensors, the key advantage of the multichannel architecture reported here is physical separation of the ECL reporting cocktail and the solution containing the target. This prevents chemical interference between the two channels.
A Strategy for Identification of Oligosaccharide Structures Using Observational Multistage Mass Spectral Library (2005)

Glycosylation is the most widespread posttranslational modification in eukaryotes; however, the role of oligosaccharides attached to proteins has been little studied because of the lack of a sensitive and easy analytical method for oligosaccharide structures. Recently, tandem mass spectrometric techniques have been revealing that oligosaccharides might have characteristic signal intensity profiles. We describe here a strategy for the rapid and accurate identification of the oligosaccharide structures on glycoproteins using only mass spectrometry. It is based on a comparison of the signal intensity profiles of multistage tandem mass (MSn) spectra between the analyte and a library of observational mass spectra acquired from structurally defined oligosaccharides prepared using glycosyltransferases. To smartly identify the oligosaccharides released from biological materials, a computer suggests which ion among the fragment ions in the MS/MS spectrum should yield the most informative MS3 spectrum to distinguish similar oligosaccharides. Using this strategy, we were able to identify the structure of N-linked oligosaccharides in immunoglobulin G as an example.
Tissue and Spatial Distribution of Flavonol and Peroxidase in Onion Bulbs and Stability of Flavonol Glucosides during Boiling of the Scales (1998)

Two major flavonol glycosides [quercetin 3,4‘-diglucoside (F1) and quercetin 4‘-monoglucoside (F2)] and a flavonol aglycon quercetin were mainly localized in the abaxial epidermis of scales. Their contents increased on aging. Peroxidase in scales oxidized flavonols in the order quercetin ≫ F2 > isoquercetin ≫ F1, and the activity was higher in the outer than in the inner scales. These results suggest that the enzyme can participate in the formation of defense substances against infection and brown compounds in the dry skin from quercetin. Contents of F1 and F2 in scales were decreased by cooking by boiling. This decrease was due to the release of F1 and F2 into cooking water and their oxidation. F2 was oxidized more rapidly than F1 during cooking. The difference in the stability between F1 and F2 was due to the presence or absence of a hydroxyl group at the C-3 position of the glucosides. Keywords: Flavonols; peroxidase; distribution in tissues; thermostability; onion (Allium cepa)