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Characterization of the small molecule ARC39, a direct and specific inhibitor of acid sphingomyelinase in vitro

Eyad Naser
Mar 10, 2020; 0:jlr.RA120000682v1-jlr.RA120000682
Research Articles




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Characterization of the small molecule ARC39, a direct and specific inhibitor of acid sphingomyelinase in vitro [Research Articles]

Inhibition of acid sphingomyelinase (ASM), a lysosomal enzyme that catalyzes the hydrolysis of sphingomyelin into ceramide and phosphorylcholine, may serve as an investigational tool or a therapeutic intervention to control many diseases. Specific ASM inhibitors are currently not sufficiently characterized. Here, we found that 1-aminodecylidene bis-phosphonic acid (ARC39) specifically and efficiently (>90%) inhibits both lysosomal and secretory ASM in vitro. Results from investigating sphingomyelin phosphodiesterase 1 (SMPD1/Smpd1) mRNA and ASM protein levels suggested that ARC39 directly inhibits ASM’s catalytic activity in cultured cells, a mechanism which differs from that of functional inhibitors of ASM (FIASMAs). We further provide evidence that ARC39 dose- and time-dependently inhibits lysosomal ASM in intact cells, and we show that ARC39 also reduces platelet- and ASMpromoted adhesion of tumor cells. The observed toxicity of ARC39 is low at concentrations relevant for ASM inhibition in vitro, and it does not strongly alter the lysosomal compartment or induce phospholipidosis in vitro. When applied intraperitoneally in vivo, even subtoxic high doses administered short-term induced sphingomyelin accumulation only locally in the peritoneal lavage without significant accumulation in plasma, liver, spleen or brain. These findings require further investigation with other possible chemical modifications. In conclusion, our results indicate that ARC39 potently and selectively inhibits ASM in vitro and highlight the need for developing compounds that can reach tissue concentrations sufficient for ASM inhibition in vivo.




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Characterization of signaling pathways associated with pancreatic {beta}-cell adaptive flexibility in compensation of obesity-linked diabetes in db/db mice [Research]

The onset of obesity-linked type 2 diabetes (T2D) is marked by an eventual failure in pancreatic β-cell function and mass that is no longer able to compensate for the inherent insulin resistance and increased metabolic load intrinsic to obesity. However, in a commonly used model of T2D, the db/db mouse, β-cells have an inbuilt adaptive flexibility enabling them to effectively adjust insulin production rates relative to the metabolic demand. Pancreatic β-cells from these animals have markedly reduced intracellular insulin stores, yet high rates of (pro)insulin secretion, together with a substantial increase in proinsulin biosynthesis highlighted by expanded rough endoplasmic reticulum and Golgi apparatus. However, when the metabolic overload and/or hyperglycemia is normalized, β-cells from db/db mice quickly restore their insulin stores and normalize secretory function. This demonstrates the β-cell’s adaptive flexibility and indicates that therapeutic approaches applied to encourage β-cell rest are capable of restoring endogenous β-cell function. However, mechanisms that regulate β-cell adaptive flexibility are essentially unknown. To gain deeper mechanistic insight into the molecular events underlying β-cell adaptive flexibility in db/db β-cells, we conducted a combined proteomic and post-translational modification specific proteomic (PTMomics) approach on islets from db/db mice and wild-type controls (WT) with or without prior exposure to normal glucose levels. We identified differential modifications of proteins involved in redox homeostasis, protein refolding, K48-linked deubiquitination, mRNA/protein export, focal adhesion, ERK1/2 signaling, and renin-angiotensin-aldosterone signaling, as well as sialyltransferase activity, associated with β-cell adaptive flexibility. These proteins are all related to proinsulin biosynthesis and processing, maturation of insulin secretory granules, and vesicular trafficking—core pathways involved in the adaptation of insulin production to meet metabolic demand. Collectively, this study outlines a novel and comprehensive global PTMome signaling map that highlights important molecular mechanisms related to the adaptive flexibility of β-cell function, providing improved insight into disease pathogenesis of T2D.




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Characterization of Prenylated C-terminal Peptides Using a Thiopropyl-based Capture Technique and LC-MS/MS [Research]

Post-translational modifications play a critical and diverse role in regulating cellular activities. Despite their fundamentally important role in cellular function, there has been no report to date of an effective generalized approach to the targeting, extraction and characterization of the critical c-terminal regions of natively prenylated proteins. Various chemical modification and metabolic labelling strategies in cell culture have been reported. However, their applicability is limited to cell culture systems and does not allow for analysis of tissue samples. The chemical characteristics (hydrophobicity, low abundance, highly basic charge) of many of the c-terminal regions of prenylated proteins have impaired the use of standard proteomic workflows. In this context, we sought a direct approach to the problem in order to examine these proteins in tissue without the use of labelling.  Here we demonstrate that prenylated proteins can be captured on chromatographic resins functionalized with mixed disulfide functions. Protease treatment of resin-bound proteins using chymotryptic digestion revealed peptides from many known prenylated proteins. Exposure of the protease-treated resin to reducing agents and hydro organic mixtures released c-terminal peptides with intact prenyl groups along with other enzymatic modifications expected in this protein family. Database and search parameters were selected to allow for c-terminal modifications unique to these molecules such as CAAX box processing and c-terminal methylation. In summary, we present a direct approach to enrich and obtain information at a molecular level of detail about prenylation of proteins from tissue and cell extracts using high performance LCMS without the need for metabolic labeling and derivatization.




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Problem Notes for SAS®9 - 65940: You might receive "ERROR: PI Point not found" when you query a PI tag name that contains a special character such as an ampersand (&)

When you query a PI tag name or element that contains a special character, such as an ampersand (&), you might receive the following error:



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Problem Notes for SAS®9 - 65834: PROC METADATA returns various errors when the input contains certain multi-byte characters

The METADATA procedure might return an error similar to one of the following:

  • ERROR: Missing root element definition.
  • Full Article


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    Problem Notes for SAS®9 - 65935: The UNICODE function does not support Numeric Character Representation (NCR) for a surrogate pair

    Using the NCR form of a surrogate pair as an input string to the UNICODE function does not convert the string to the appropriate display character.




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    Clinical characteristics of 113 deceased patients with coronavirus disease 2019: retrospective study




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    Atomic force microscopy-based characterization of the interaction of PriA helicase with stalled DNA replication forks [DNA and Chromosomes]

    In bacteria, the restart of stalled DNA replication forks requires the DNA helicase PriA. PriA can recognize and remodel abandoned DNA replication forks, unwind DNA in the 3'-to-5' direction, and facilitate the loading of the helicase DnaB onto the DNA to restart replication. Single-stranded DNA–binding protein (SSB) is typically present at the abandoned forks, but it is unclear how SSB and PriA interact, although it has been shown that the two proteins interact both physically and functionally. Here, we used atomic force microscopy to visualize the interaction of PriA with DNA substrates with or without SSB. These experiments were done in the absence of ATP to delineate the substrate recognition pattern of PriA before its ATP-catalyzed DNA-unwinding reaction. These analyses revealed that in the absence of SSB, PriA binds preferentially to a fork substrate with a gap in the leading strand. Such a preference has not been observed for 5'- and 3'-tailed duplexes, suggesting that it is the fork structure that plays an essential role in PriA's selection of DNA substrates. Furthermore, we found that in the absence of SSB, PriA binds exclusively to the fork regions of the DNA substrates. In contrast, fork-bound SSB loads PriA onto the duplex DNA arms of forks, suggesting a remodeling of PriA by SSB. We also demonstrate that the remodeling of PriA requires a functional C-terminal domain of SSB. In summary, our atomic force microscopy analyses reveal key details in the interactions between PriA and stalled DNA replication forks with or without SSB.




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    Immigrants and WIOA Services: Comparison of Sociodemographic Characteristics of Native- and Foreign-Born Adults in the United States

    As federal and state governments ramp up efforts to implement the Workforce Innovation and Opportunity Act, these fact sheets compare key characteristics of the foreign born and the U.S. born that are relevant to understanding needs for adult education and workforce training services. The fact sheets cover the United States, the 20 states and 25 counties with the largest immigrant populations, and New York City.




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    Loss of Incretin Effect Is a Specific, Important, and Early Characteristic of Type 2 Diabetes

    Jens J. Holst
    May 1, 2011; 34:S251-S257
    Diabetes Treatments




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    Characterization of Renal Glucose Reabsorption in Response to Dapagliflozin in Healthy Subjects and Subjects With Type 2 Diabetes

    Ralph A. DeFronzo
    Oct 1, 2013; 36:3169-3176
    Emerging Technologies and Therapeutics




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    Depressive Symptoms in Children and Adolescents With Type 1 Diabetes: Association with diabetes-specific characteristics

    Korey K. Hood
    Jun 1, 2006; 29:1389-1389
    BR Epidemiology/Health Services/Psychosocial Research




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    [Prayers of magical character]

    18th century.




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    [Prayers of magical character]

    18th - 19th century.




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    [Prayers of magical character]

    18th century.




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    [Prayers of magical character]

    18th century.




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    [Prayers of magical character]

    18th - 19th century.




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    [Prayers of magical character]

    19th century.




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    [Prayers of magical character]

    19th century.




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    [Prayers of magical character]

    19th century.




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    [Prayers of magical character]

    19th century.




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    [Prayers of magical character]

    19th century.




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    [Prayers of magical character]

    19th century.




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    [Prayers of magical character]

    19th century.




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    [Prayers of magical character]

    19th century.




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    [Prayers of magical character]

    19th century.




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    [Prayers of magical character]

    19th century.




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    [Accounts of medical and magical character, fortune tellings and predictions]

    19th century.




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    [Prayers of magical character]

    19th century.




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    [Prayers of magical character]

    19th century.




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    [Prayers of magical character]

    18th - 19th century.




    character

    [Prayers of magical character]

    18th - 19th century.




    character

    [Prayers of magical character]

    18th century.




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    A descriptive list of anthropometric apparatus : consisting of instruments for measuring and testing the chief physical characteristics of the human body.

    Cambridge : printed by C.J. Clay at the University Press, 1887.




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    Dr. Buchans Domestic medicine; or a treatise on the prevention and cure of diseases, by regimen and simple medicines. To which is added, characteristic symptoms of diseases, from the nosology of the late celebrated Dr. Cullen of Edinburgh. With an appendi

    Newcastle : printed by K. Anderson, 1812.




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    An episode in 'Every man in his humour' by Ben Jonson: Charles Dickens in character as Captain Bobadill is awakened after a hard night's drinking. Lithograph by T.H. Maguire after C.R. Leslie.

    [London?]




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    William Macready in character as Werner in the play Werner by Lord Byron. Engraving by C.W. Sharpe after D. Maclise.

    [London?]




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    Drug abuse treatment client characteristics and pretreatment behaviors : 1979-1981 TOPS admission cohorts / Robert L. Hubbard, Robert M. Bray, Elizabeth R. Cavanaugh, J. Valley Rachal, S. Gail Craddock, James J. Collins, Margaret Allison ; Research Triang

    Rockville, Maryland : National Institute on Drug Abuse, 1986.




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    Psychosocial characteristics of drug-abusing women / by Marvin R. Burt, principal investigator ; Thomas J. Glynn, Barbara J. Sowder ; Burt Associates, Inc.

    Rockville, Maryland : National Institute on Drug Abuse, 1979.




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    Stein characterizations for linear combinations of gamma random variables

    Benjamin Arras, Ehsan Azmoodeh, Guillaume Poly, Yvik Swan.

    Source: Brazilian Journal of Probability and Statistics, Volume 34, Number 2, 394--413.

    Abstract:
    In this paper we propose a new, simple and explicit mechanism allowing to derive Stein operators for random variables whose characteristic function satisfies a simple ODE. We apply this to study random variables which can be represented as linear combinations of (not necessarily independent) gamma distributed random variables. The connection with Malliavin calculus for random variables in the second Wiener chaos is detailed. An application to McKay Type I random variables is also outlined.




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    A primer on the characterization of the exchangeable Marshall–Olkin copula via monotone sequences

    Natalia Shenkman.

    Source: Brazilian Journal of Probability and Statistics, Volume 34, Number 1, 127--135.

    Abstract:
    While derivations of the characterization of the $d$-variate exchangeable Marshall–Olkin copula via $d$-monotone sequences relying on basic knowledge in probability theory exist in the literature, they contain a myriad of unnecessary relatively complicated computations. We revisit this issue and provide proofs where all undesired artefacts are removed, thereby exposing the simplicity of the characterization. In particular, we give an insightful analytical derivation of the monotonicity conditions based on the monotonicity properties of the survival probabilities.




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    Efficient Characterization of Dynamic Response Variation Using Multi-Fidelity Data Fusion through Composite Neural Network. (arXiv:2005.03213v1 [stat.ML])

    Uncertainties in a structure is inevitable, which generally lead to variation in dynamic response predictions. For a complex structure, brute force Monte Carlo simulation for response variation analysis is infeasible since one single run may already be computationally costly. Data driven meta-modeling approaches have thus been explored to facilitate efficient emulation and statistical inference. The performance of a meta-model hinges upon both the quality and quantity of training dataset. In actual practice, however, high-fidelity data acquired from high-dimensional finite element simulation or experiment are generally scarce, which poses significant challenge to meta-model establishment. In this research, we take advantage of the multi-level response prediction opportunity in structural dynamic analysis, i.e., acquiring rapidly a large amount of low-fidelity data from reduced-order modeling, and acquiring accurately a small amount of high-fidelity data from full-scale finite element analysis. Specifically, we formulate a composite neural network fusion approach that can fully utilize the multi-level, heterogeneous datasets obtained. It implicitly identifies the correlation of the low- and high-fidelity datasets, which yields improved accuracy when compared with the state-of-the-art. Comprehensive investigations using frequency response variation characterization as case example are carried out to demonstrate the performance.




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    Characterization of nanoencapsulated food ingredients

    9780128156681 (electronic bk.)




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    Averages of unlabeled networks: Geometric characterization and asymptotic behavior

    Eric D. Kolaczyk, Lizhen Lin, Steven Rosenberg, Jackson Walters, Jie Xu.

    Source: The Annals of Statistics, Volume 48, Number 1, 514--538.

    Abstract:
    It is becoming increasingly common to see large collections of network data objects, that is, data sets in which a network is viewed as a fundamental unit of observation. As a result, there is a pressing need to develop network-based analogues of even many of the most basic tools already standard for scalar and vector data. In this paper, our focus is on averages of unlabeled, undirected networks with edge weights. Specifically, we (i) characterize a certain notion of the space of all such networks, (ii) describe key topological and geometric properties of this space relevant to doing probability and statistics thereupon, and (iii) use these properties to establish the asymptotic behavior of a generalized notion of an empirical mean under sampling from a distribution supported on this space. Our results rely on a combination of tools from geometry, probability theory and statistical shape analysis. In particular, the lack of vertex labeling necessitates working with a quotient space modding out permutations of labels. This results in a nontrivial geometry for the space of unlabeled networks, which in turn is found to have important implications on the types of probabilistic and statistical results that may be obtained and the techniques needed to obtain them.




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    A hidden Markov model approach to characterizing the photo-switching behavior of fluorophores

    Lekha Patel, Nils Gustafsson, Yu Lin, Raimund Ober, Ricardo Henriques, Edward Cohen.

    Source: The Annals of Applied Statistics, Volume 13, Number 3, 1397--1429.

    Abstract:
    Fluorescing molecules (fluorophores) that stochastically switch between photon-emitting and dark states underpin some of the most celebrated advancements in super-resolution microscopy. While this stochastic behavior has been heavily exploited, full characterization of the underlying models can potentially drive forward further imaging methodologies. Under the assumption that fluorophores move between fluorescing and dark states as continuous time Markov processes, the goal is to use a sequence of images to select a model and estimate the transition rates. We use a hidden Markov model to relate the observed discrete time signal to the hidden continuous time process. With imaging involving several repeat exposures of the fluorophore, we show the observed signal depends on both the current and past states of the hidden process, producing emission probabilities that depend on the transition rate parameters to be estimated. To tackle this unusual coupling of the transition and emission probabilities, we conceive transmission (transition-emission) matrices that capture all dependencies of the model. We provide a scheme of computing these matrices and adapt the forward-backward algorithm to compute a likelihood which is readily optimized to provide rate estimates. When confronted with several model proposals, combining this procedure with the Bayesian Information Criterion provides accurate model selection.




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    A characterization of the finiteness of perpetual integrals of Lévy processes

    Martin Kolb, Mladen Savov.

    Source: Bernoulli, Volume 26, Number 2, 1453--1472.

    Abstract:
    We derive a criterium for the almost sure finiteness of perpetual integrals of Lévy processes for a class of real functions including all continuous functions and for general one-dimensional Lévy processes that drifts to plus infinity. This generalizes previous work of Döring and Kyprianou, who considered Lévy processes having a local time, leaving the general case as an open problem. It turns out, that the criterium in the general situation simplifies significantly in the situation, where the process has a local time, but we also demonstrate that in general our criterium can not be reduced. This answers an open problem posed in ( J. Theoret. Probab. 29 (2016) 1192–1198).




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    Characterization of probability distribution convergence in Wasserstein distance by $L^{p}$-quantization error function

    Yating Liu, Gilles Pagès.

    Source: Bernoulli, Volume 26, Number 2, 1171--1204.

    Abstract:
    We establish conditions to characterize probability measures by their $L^{p}$-quantization error functions in both $mathbb{R}^{d}$ and Hilbert settings. This characterization is two-fold: static (identity of two distributions) and dynamic (convergence for the $L^{p}$-Wasserstein distance). We first propose a criterion on the quantization level $N$, valid for any norm on $mathbb{R}^{d}$ and any order $p$ based on a geometrical approach involving the Voronoï diagram. Then, we prove that in the $L^{2}$-case on a (separable) Hilbert space, the condition on the level $N$ can be reduced to $N=2$, which is optimal. More quantization based characterization cases in dimension 1 and a discussion of the completeness of a distance defined by the quantization error function can be found at the end of this paper.




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    The fourth characteristic of a semimartingale

    Alexander Schnurr.

    Source: Bernoulli, Volume 26, Number 1, 642--663.

    Abstract:
    We extend the class of semimartingales in a natural way. This allows us to incorporate processes having paths that leave the state space $mathbb{R}^{d}$. In particular, Markov processes related to sub-Markovian kernels, but also non-Markovian processes with path-dependent behavior. By carefully distinguishing between two killing states, we are able to introduce a fourth semimartingale characteristic which generalizes the fourth part of the Lévy quadruple. Using the probabilistic symbol, we analyze the close relationship between the generators of certain Markov processes with killing and their (now four) semimartingale characteristics.




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    The Pain of Sleep Loss: A Brain Characterization in Humans

    Adam J. Krause
    Mar 20, 2019; 39:2291-2300
    BehavioralSystemsCognitive